What's the opposite of skipping steps?

My 3 axis router developed an interesting issue a while ago and after a lot of experimentation I'm pretty sure the problem is with the 7i96s.
The first thing that went wrong was that the X axis started moving more than it should. According to math the steps/mm should be 480, but suddenly something decided that about 455 is the correct number. On it's own, that wouldn't be much of a problem, but it seems to occasionally switch to a different number and loose its position.
I have tried the following:
- different acceleration settings (it happily did 3000mm/s2 for a while, returning to within 0,01mm, but sometimes lost steps at 250mm/s2) 
- different stepper drivers, both open and closed loop
- different wiring between the 7i96s and driver
- new linuxcnc installation
- flashed the firmware to the 7i96s again
- completely new configuration through pncconf
- moved x axis from stepgen 0 to stepgen 4

The other axis work perfectly everytime and for about a year so did X, at 480 steps/mm. Z axis has the same motor, driver and encoder as X.
I have access to a 7i96 and I will try it out on friday, but I still want to ask if anyone has a different idea for what could cause this?

If the problem stays with the X axis with motor driver and 7I96S channel changes,
it really sounds like the issue is more likely to be mechanical than electrical.