Yup i got same comm error few times and for me it seems to happen mostly for the files that wont slice with home.
I am using SF41 and sender is repsnapper (kulitorum version) with gen3 electronics.
For tests i detached cables from extruder motor and tried the print with heater off, and yes its in same place.
Although i didnt bothered with that any further, maybe stl needs repair or something so cant say its all about SF,
About the Z and acceleration, in gcodes in layer changes area strange things seem to happen if tampering with various speeds, including retract. I guess retract sets speed to retract, retracts, then sets the feed/flow speed, thinking a new extruder forward move comes next (as usually would). When its a Z move and it tends to start decelerate from that speed. However some layers do look right (no clue why), but not for an entire gcode, just some parts of it. I would like acceleration back tho so dunno how to hotfix it, other than setting the feed rate to something acceptable for Z, which would be a bummer.
