Other than the optic boards, the only thing else "electronics" is the harness itself (which is what the "tech" recommended the first time to me). At $7.50 for the harness, it may behoove you to try it out. I may actually call and order one just in case anyway.
Unless a mouse chewed it, or it got yanked, a cable isn't going to go bad. Even if it did, it would more likely just lose an entire axis. I'd say re-seat the cables a few times on the connectors and if nothing changes, then it's safe to assume the cables aren't the problem.
If the boards are good, and they just may not be, then start looking at the system. Sometimes viruses and other system issues can affect the mouse polling speeds. It shouldn't matter with newer versions of MAME, but make sure no-one has messed with the mouse settings in your OS, or made any other changes to the system (installation of new software, etc) that might coincide with the issue.
Frizz, your problem is definitely hardware, as it's only one axis. In a situation where both are affected the same way, all of a sudden and for no particular reason, then start suspecting other causes.
RandyT