Not so sure unit values would be the issue, as it should return to the same 0,0, but sizes would be wrong.
What kind of hour long files are you running, 3D/v-carve? Are your ramp settings set to default or are you using some more aggressive settings? With a standard, you can lose steps if direction changes are too abrupt. If you 'soften' the ramp settings, you can alleviate that. This is mostly noticeable with 3D files, but could show up on v-carving or a lot of short quick raster movements.
If your communications were bad, you'd be seeing other errors, but it would be a good check to see what your packet et values are. Read up on the diagnostics for v3.8.XX under help/notes....
If you drop the motors from the rack, does the gantry/y car roll freely all over, no binding in the y car from side to side. When putting the motors back in place, just firm hand pressure is sufficient, no clamping force of the motors to the rack is needed.
If guns kill people, I guess pencils misspell words, cars drive drunk and spoons make people fat.
"Those who hammer their guns into plows, will plow for those who do not" - Thomas Jefferson