The zig-zag in stellarium/CdC is not necessarily real. While the AstroEQ is keeping track of the current encoder value internally, EQMOD is only polling this periodically (typically ~5 times a second). That means that as far as it any planetarium is concerned, the mount stops for 200ms, then moves a chunk, then stops for 200ms, then moves another chunk. This essentially means that it appears to oscillate in the RA axis. This is quite normal, and not representative of what the mount is actually doing.
The step rate from the AstroEQ is pretty constant - there is some minor dithering for improved accuracy, but that is only +/-500ns added to certain pulses to account for rounding errors which should not be noticeable at all.
This is one of those weird cases where two things seem to corresponding to each other, but are actually most likely unrelated.
If the mount is not moving smoothly it's likely the issue raised in the other thread with the motors not handling the microstepping well, something which can be mitigated as shown in the other thread.