@dc42 I don't think that is true, or at least not for the one that I have. My printer is on linear rails driven by a belt. That goes for all axis'. I originally modeled my config file off of CNC Kitchen's config for his Cetus, https://youtu.be/WcPyujDF2eU, video for reference. It still gave me the loud noise when operating the stepper motors. I will try to lower the speed and acceleration. Hopefully that works. Thank you all for the help.

@deckingman they are essential with slight variations to there model number. For instance the y stepper motor end in 01N instead of 02N and the Z is 03N. The stepper motor current is set so high on the extruder is because I'm using the orbiter V1.5 and that's there recommended current usage. I will try to up the current and see if that helps.

@phaedrux So what are my options here? Do i need to replace the stepper motors or is this going to happen with any system that I plug into the Duet 3?

@deckingman I would to provide information on the stepper motors but, unfortunately there is no information on these stepper motors. I already looked online for the model number/manufacturer but there is no info. Ill add a picture of the stepper motor for reference.

@phaedrux I enabled stealth chop and its still making the noise, albeit more quite but, it is still significantly louder than expected.

@phaedrux yes it does. I will try to implement that into my printer thank you very much for the help. Just out of curiosity, why does the noise happen from this board? I've ran the machine with its original mainboard, as well as a Mellow Fly E3, and they both sounded alot better in this situation. Is it the stepper motors or something?

@phaedrux That makes sense. 20220628_180132.mp4 here is a quick video of the noise generated by the board (only when the stepper motors are active). My current configuration
; Configuration file for Duet 3 Mini 5+ (firmware version 3.3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v3.3.10 on Sun Jun 26 2022 16:52:21 GMT-0700 (Pacific Daylight Time)

; General preferences
G90 ; send absolute coordinates...
M83 ; ...but relative extruder moves
M550 P"CETUS MK3" ; set printer name

; Network
M551 P"" ; set password
M552 S1 ; enable network
M586 P0 S1 ; enable HTTP
M586 P1 S0 ; disable FTP
M586 P2 S0 ; disable Telnet

; Drives
M569 P0.0 S1 ; physical drive 0.0 goes forwards
M569 P0.1 S1 ; physical drive 0.1 goes forwards
M569 P0.2 S1 ; physical drive 0.2 goes forwards
M569 P0.3 S1 ; physical drive 0.3 goes forwards
M584 X0.0 Y0.1 Z0.2 E0.3 ; set drive mapping
M350 X32 Y32 Z32 E32 I1 ; configure microstepping with interpolation
M92 X180.00 Y180.00 Z180.00 E690.00 ; set steps per mm
M566 X900.00 Y900.00 Z600.00 E600.00 ; set maximum instantaneous speed changes (mm/min)
M203 X12000.00 Y12000.00 Z12000.00 E7200.00 ; set maximum speeds (mm/min)
M201 X150.00 Y150.00 Z150.00 E800.00 ; set accelerations (mm/s^2)
M906 X400 Y400 Z450 E1200 I10 ; set motor currents (mA) and motor idle factor in per cent
M84 S30 ; Set idle timeout

; Axis Limits
M208 X0 Y0 Z0 S1 ; set axis minima
M208 X180 Y180 Z175 S0 ; set axis maxima

; Endstops
M574 X2 S1 P"io5.in" ; configure switch-type (e.g. microswitch) endstop for high end on X via pin io5.in
M574 Y2 S1 P"io6.in" ; configure switch-type (e.g. microswitch) endstop for high end on Y via pin io6.in
M574 Z2 S1 P"io2.in" ; configure switch-type (e.g. microswitch) endstop for high end on Z via pin io2.in

; Z-Probe
M558 P0 H5 F120 T6000 ; disable Z probe but set dive height, probe speed and travel speed
M557 X15:165 Y15:165 S50 ; define mesh grid

; Heaters
M140 H-1 ; disable heated bed (overrides default heater mapping)
M308 S0 P"temp0" Y"thermistor" T100000 B4725 C7.06e-8 ; configure sensor 0 as thermistor on pin temp0
M950 H0 C"out1" T0 ; create nozzle heater output on out1 and map it to sensor 0
M307 H0 B0 S1.00 ; disable bang-bang mode for heater and set PWM limit
M143 H0 S300 ; set temperature limit for heater 0 to 300C

; Fans
M950 F0 C"out3" Q500 ; create fan 0 on pin out3 and set its frequency
M106 P0 S0 H-1 ; set fan 0 value. Thermostatic control is turned off
M950 F1 C"out4" Q500 ; create fan 1 on pin out4 and set its frequency
M106 P1 S0 H1:0 T45 ; set fan 1 value. Thermostatic control is turned on

; Tools
M563 P0 D0 F0 ; define tool 0
G10 P0 X0 Y0 Z0 ; set tool 0 axis offsets
G10 P0 R0 S0 ; set initial tool 0 active and standby temperatures to 0C

; Custom settings are not defined

@mikeabuilder Just lowered the interpolation to 16 and I would move the motors at all or at least it struggled to move them. I originally had it set to 32 and it worked moving the motors but the mainboard is making a loud noise, or at least it sounds like its the mainboard.

@phaedrux The only reason I put such a high microstepping is because as I mentioned above, I found a post on this forum with the config files for the cetus and I copy and pasted most of the config. I originally started at 32 but it still gave the loud noise. I will try lowering ever further. Here is the results of the M122 command.
M122
=== Diagnostics ===
RepRapFirmware for Duet 3 Mini 5+ version 3.4.1 (2022-06-01 21:06:56) running on Duet 3 Mini5plus WiFi (standalone mode)
Board ID: 4J3NN-Q396U-D65J0-40KMS-3413Z-760H1
Used output buffers: 3 of 40 (13 max)
=== RTOS ===
Static ram: 103684
Dynamic ram: 109888 of which 12 recycled
Never used RAM 28128, free system stack 206 words
Tasks: NETWORK(ready,10.7%,267) HEAT(notifyWait,0.0%,358) Move(notifyWait,0.0%,363) CanReceiv(notifyWait,0.0%,942) CanSender(notifyWait,0.0%,372) CanClock(delaying,0.0%,339) TMC(notifyWait,0.7%,114) MAIN(running,85.7%,412) IDLE(ready,2.0%,29) AIN(delaying,0.9%,274), total 100.0%
Owned mutexes: WiFi(NETWORK)
=== Platform ===
Last reset 00:00:11 ago, cause: software
Last software reset at 2022-06-28 17:45, reason: User, GCodes spinning, available RAM 28128, slot 0
Software reset code 0x0003 HFSR 0x00000000 CFSR 0x00000000 ICSR 0x00000000 BFAR 0xe000ed38 SP 0x00000000 Task MAIN Freestk 0 n/a
Error status: 0x00
MCU revision 3, ADC conversions started 11579, completed 11579, timed out 0, errs 0
Step timer max interval 752
MCU temperature: min 31.7, current 32.6, max 32.6
Supply voltage: min 24.1, current 24.2, max 24.2, under voltage events: 0, over voltage events: 0, power good: yes
Heap OK, handles allocated/used 0/0, heap memory allocated/used/recyclable 0/0/0, gc cycles 0
Events: 0 queued, 0 completed
Driver 0: standstill, SG min 0, read errors 0, write errors 1, ifcnt 19, reads 567, writes 9, timeouts 0, DMA errors 0, CC errors 0
Driver 1: standstill, SG min 0, read errors 0, write errors 1, ifcnt 19, reads 567, writes 9, timeouts 0, DMA errors 0, CC errors 0
Driver 2: standstill, SG min 0, read errors 0, write errors 1, ifcnt 19, reads 567, writes 9, timeouts 0, DMA errors 0, CC errors 0
Driver 3: standstill, SG min 0, read errors 0, write errors 1, ifcnt 19, reads 566, writes 9, timeouts 0, DMA errors 0, CC errors 0
Driver 4: standstill, SG min 0, read errors 0, write errors 1, ifcnt 19, reads 567, writes 9, timeouts 0, DMA errors 0, CC errors 0
Driver 5: not present
Driver 6: not present
Date/time: 2022-06-28 17:45:24
Cache data hit count 22382075
Slowest loop: 11.27ms; fastest: 0.13ms
=== Storage ===
Free file entries: 10
SD card 0 detected, interface speed: 22.5MBytes/sec
SD card longest read time 3.3ms, write time 0.0ms, max retries 0
=== Move ===
DMs created 83, segments created 0, maxWait 0ms, bed compensation in use: none, comp offset 0.000
=== MainDDARing ===
Scheduled moves 0, completed 0, hiccups 0, stepErrors 0, LaErrors 0, Underruns [0, 0, 0], CDDA state -1
=== AuxDDARing ===
Scheduled moves 0, completed 0, hiccups 0, stepErrors 0, LaErrors 0, Underruns [0, 0, 0], CDDA state -1
=== Heat ===
Bed heaters -1 -1 -1 -1, chamber heaters -1 -1 -1 -1, ordering errs 0
=== GCodes ===
Segments left: 0
Movement lock held by null
HTTP is idle in state(s) 0
Telnet is idle in state(s) 0
File is idle in state(s) 0
USB is idle in state(s) 0
Aux is idle in state(s) 0
Trigger is idle in state(s) 0
Queue is idle in state(s) 0
LCD is idle in state(s) 0
SBC is idle in state(s) 0
Daemon is idle in state(s) 0
Aux2 is idle in state(s) 0
Autopause is idle in state(s) 0
Code queue is empty
=== CAN ===
Messages queued 99, received 0, lost 0, boc 0
Longest wait 0ms for reply type 0, peak Tx sync delay 0, free buffers 18 (min 18), ts 56/0/0
Tx timeouts 0,0,55,0,0,42 last cancelled message type 30 dest 127
=== Network ===
Slowest loop: 17.05ms; fastest: 0.00ms
Responder states: HTTP(0) HTTP(0) HTTP(0) HTTP(0) FTP(0) Telnet(0), 0 sessions
HTTP sessions: 1 of 8

• WiFi -
  Network state is active
  WiFi module is connected to access point
  Failed messages: pending 0, notready 0, noresp 0
  WiFi firmware version 1.26
  WiFi MAC address d8:bf:c0:15:09:ca
  WiFi Vcc 3.35, reset reason Power up
  WiFi flash size 2097152, free heap 25224
  WiFi IP address 192.168.1.162
  WiFi signal strength -55dBm, mode 802.11n, reconnections 0, sleep mode modem
  Clock register 00002002
  Socket states: 0 0 0 0 0 0 0 0

@jay_s_uk Im using moons motors type:17HT4003-02N(I believe the stepper motors are made special for the Cetus because I already looked for the model number online). I have the version 1.01 of duet mini 5+ Wifi. The config file is in the top line. Im not sure how to show the whole config on the page.