Just another data point: I am having a similar problem on a CoreXY setup, Mini5+ and 0.9 motors. The printer worked perfectly with a Duet2 but will randomly (and loudly!) skip steps with a Mini5+.
I have raised the motor amps and lowered jerk a lot (M566), reduced travel & print speed in the slicer, forced spreadCycle mode all the time on XY but still I get skipping, exactly like @carcamerarig describes (suddenly a loud "thump" and then there is a major layer shift). It is random, sometimes I can finish a small print but usually not.
I see this in the M122 dump, could it be related? Write errors, timeouts, failedOps...
Driver 0: position 99200, standstill, SG min/max 0/54, read errors 0, write errors 1, ifcnt 59, reads 53605, writes 19, timeouts 184, DMA errors 0, failedOp 0x41
Driver 1: position 0, standstill, SG min/max 0/52, read errors 0, write errors 1, ifcnt 59, reads 53758, writes 19, timeouts 31, DMA errors 0, failedOp 0x72
Driver 2: position 5755, standstill, SG min/max 0/56, read errors 0, write errors 1, ifcnt 58, reads 53596, writes 18, timeouts 194, DMA errors 0, failedOp 0x6f
Driver 3: position 0, standstill, SG min/max 0/56, read errors 0, write errors 1, ifcnt 58, reads 53650, writes 19, timeouts 138, DMA errors 0, failedOp 0x6f
Driver 4: position 0, standstill, SG min/max 0/62, read errors 0, write errors 1, ifcnt 41, reads 53792, writes 13, timeouts 3, DMA errors 0, failedOp 0x01
Driver 5: position 0, standstill, SG min/max 0/510, read errors 0, write errors 1, ifcnt 55, reads 53598, writes 18, timeouts 192, DMA errors 0, failedOp 0x72
Driver 6: position 0, standstill, SG min/max 0/496, read errors 0, write errors 1, ifcnt 55, reads 53787, writes 18, timeouts 3, DMA errors 0, failedOp 0x41
I tried upgrading from 3.2.2 to 3.3b2 and that made no difference, skipping is still random.
