Thanks @deckingman, appreciate your help and gave your suggestions a try this morning. Good to know that M584 returns the drive mapping. I changed the M584 to define all drives every time in config.g and homez.g.
After config.g M584 -> Driver assignments: X0 Y1 Z2:3:4 U3 V4 E5, 3 axes visible
After homez.g M584 -> Driver assignments: X0 Y1 Z2:3:4 U3 V4 E5, 3 axes visible

Behavior is still the same. Running Homez.g the first time after firmware reset and everything works as expected, with the Z, U and V axes rotating the same direction. But when Homez is run a second time, the first G1 Z400 U400 V400 F500 S1 command causes the Z axis to rotate in different direction from U and V. Homez then hangs for a couple of minutes before continuing on with the G1 V-3 F200 S2, and subsequent commands.

Also tried @phaedrux suggestion to enter commands individually from console. Did this after running homez once after reset. Same behavior. Checked drive mapping after the G1 Z400 U400 V400 F500 S1 and it returned Driver assignments: X0 Y1 Z2 U3 V4 E5, 5 axes visible

The Z axis rotating in wrong direction was due to stepper current being too low. Thanks for that pointer!

Running CoreXY. Tested with firmware 2.02RC4. First Z axis move after recombining is carried out extremely slowly. Regardless of F value or distance it takes about 30 seconds to complete. I can see all three z axis motors turning very slowly.

Yes, DuetWifi + Duex5. Upgraded today to:
Firmware Version: 2.02RC4(RTOS) (2018-11-18b5)
WiFi Server Version: 1.21
Web Interface Version: 1.22.5

Pulsing is better, but there is still one big pulse upon firmware Reset on the Fan/PWM and Extruder Heater outputs on the Duet5, that are tripping the SSRs connected those modules.

Thanks for info. Cluster size is 64K.
Just upgraded today to:
Firmware Version: 2.02RC4(RTOS) (2018-11-18b5)
WiFi Server Version: 1.21
Web Interface Version: 1.22.5
Will post again if it continues to occur.
Thanks

The DuetWifi slows down and ultimately kicks out an error while uploading even small gcode files. The WIFI signal is strong at the computer and DuetWifi, which are just few feet apart. It seems to happen when there special characters in the file name (e.g. parentheses). Is there a limit to the length of the file name and are special characters allowed?

On firmware startup and after reset, the Fan PWM and Extruder heaters pulse and flicker many times. When using these to control other peripherals (e.g. lights, SSR) they peripherals all strobe 3-10 times at startup or upon reset. Is there any way to disable this pulsing of the FAN PWM and Extuder heater outputs? Thanks.

HI @dc42. Wondering if you had any further insight into this issue. Is it a firmware bug, or something with the configurations/gcode? Thanks.

@dc42 Adding M400 after M584 did not resolve the issue. In fact, adding M400 after the second M584 caused homez.g to hang.

homez.g
; Home 3 Independent Z-Axis Drives

M117 Homing Z axis...
M400 ; Wait for movement to stop

G91 ; relative positioning

M584 X0 Y1 Z2 U3 V4 E5 P5 ; separate Z axis motors. P5 to display/drive 5 axis.
M400 ; Wait for movement to stop

; The second time Homez is run, only the Z axis moves with this command (U and V do not move).
; Homez then hangs here for a couple of minutes, before continuing ...
G1 Z400 U400 V400 F500 S1 ; lower all z motors until each corresponding z-stop reached

G1 V-3 F200 S2 ; raise Z3 axis slowly (S2 Ignore endstops and ignore axis not homed)
G1 V10 F200 S1 ; lower Z3 motor slowly until its endstop reached
G1 V-3 F200 S2 ; raise Z3 axis slowly (S2 Ignore endstops and ignore axis not homed)
M400 ; Wait for movement to stop

G1 U-3 F200 S2 ; raise Z2 axis slowly (S2 Ignore endstops and ignore axis not homed)
G1 U10 F200 S1 ; lower Z2 motor slowly until its endstop reached
G1 U-3 F200 S2 ; raise Z2 axis slowly (S2 Ignore endstops and ignore axis not homed)
M400 ; Wait for movement to stop

G1 Z-3 F200 S2 ; raise Z1 axis slowly (S2 Ignore endstops and ignore axis not homed)
G1 Z10 F200 S1 ; lower Z1 motor slowly until its endstop reached
G1 Z-3 F200 S2 ; raise Z1 axis slowly (S2 Ignore endstops and ignore axis not homed)
M400 ; Wait for movement to stop

; This test move before combining axis works
G1 Z-5 U-5 V-5 F200 S2 ; raise Z1 axis slowly (S2 Ignore endstops and ignore axis not homed)
M400 ; Wait for movement to stop

M584 X0 Y1 Z2:3:4 E5 P3 ; Combine Z, U and V. P3 to display/drive 3 axis.

; Adding M400 here caused the homez.g to hang
;M400 ; Wait for movement to stop

; This test move after combining axis also works now
G1 Z-5 F200 ; test raise all axis slowly
M400 ; Wait for movement to stop

G90 ; absolute positioning
M400 ; Wait for movement to stop

M117 Homing Z axis done

Thanks for the suggestion @dc42, G91 is already there before the first M584 splitting the drives and before the G1 ZUV move in Homez.g, and the G90 is at the end.

Thanks @deckingman, appreciate your help and gave your suggestions a try this morning. Good to know that M584 returns the drive mapping. I changed the M584 to define all drives every time in config.g and homez.g.
After config.g M584 -> Driver assignments: X0 Y1 Z2:3:4 U3 V4 E5, 3 axes visible
After homez.g M584 -> Driver assignments: X0 Y1 Z2:3:4 U3 V4 E5, 3 axes visible

Behavior is still the same. Running Homez.g the first time after firmware reset and everything works as expected, with the Z, U and V axes rotating the same direction. But when Homez is run a second time, the first G1 Z400 U400 V400 F500 S1 command causes the Z axis to rotate in different direction from U and V. Homez then hangs for a couple of minutes before continuing on with the G1 V-3 F200 S2, and subsequent commands.

Also tried @phaedrux suggestion to enter commands individually from console. Did this after running homez once after reset. Same behavior. Checked drive mapping after the G1 Z400 U400 V400 F500 S1 and it returned Driver assignments: X0 Y1 Z2 U3 V4 E5, 5 axes visible

Its starting to look like a firmware bug. Upgraded to Firmware Version 2.01(RTOS) (2018-07-26b2). Now the 3 z-axis rotate in the correct direction after recombining Z, U and V. However, this only works the first time after firmware reset. If Home Z is run a second time, at the first G1 command, only the Z axis moves (U and V do not move).

homez.g
; Home 3 Independent Z-Axis Drives

M117 Homing Z axis...

M400 ; Wait for movement to stop
G91 ; relative positioning

M584 Z2 U3 V4 P5 ; separate Z axis motors. P5 to display/drive 5 axis.

; This only works the fist time after firmware reset.
; The second time Homez is run, only the Z axis moves (U and V do not move).
G1 Z400 U400 V400 F500 S1 ; lower all z motors until each corresponding z-stop reached
M400 ; Wait for movement to stop

G1 V-3 F200 S2 ; raise Z3 axis slowly (S2 Ignore endstops and ignore axis not homed)
G1 V10 F200 S1 ; lower Z3 motor slowly until its endstop reached
G1 V-3 F200 S2 ; raise Z3 axis slowly (S2 Ignore endstops and ignore axis not homed)
M400 ; Wait for movement to stop

G1 U-3 F200 S2 ; raise Z2 axis slowly (S2 Ignore endstops and ignore axis not homed)
G1 U10 F200 S1 ; lower Z2 motor slowly until its endstop reached
G1 U-3 F200 S2 ; raise Z2 axis slowly (S2 Ignore endstops and ignore axis not homed)
M400 ; Wait for movement to stop

G1 Z-3 F200 S2 ; raise Z1 axis slowly (S2 Ignore endstops and ignore axis not homed)
G1 Z10 F200 S1 ; lower Z1 motor slowly until its endstop reached
G1 Z-3 F200 S2 ; raise Z1 axis slowly (S2 Ignore endstops and ignore axis not homed)
M400 ; Wait for movement to stop

; This test move before combining axis works
G1 Z-5 U-5 V-5 F200 S2 ; raise Z1 axis slowly (S2 Ignore endstops and ignore axis not homed)

M584 Z2:3:4 P3 ; Combine Z, U and V. P3 to display/drive 3 axis.

; This test move after combining axis also works now
G1 Z-5 F200 ; test raise all axis slowly

G90 ; absolute positioning

M117 Homing Z axis done