I launched a space station into a nice stable 250x250 orbit using MechJeb2, when I came to launch my supply ship, during rendezvous I noticed my space station drifting off course. When I switched to my station the periapsis was falling and my apoapsis was increasing without any input by me and all MechJeb modules were switched off. Do you know what could be causing this?

It sounds like either (1) you accidentally increased your station's throttle slightly or (2) MechJeb left your throttle on by mistake.

It sounds like you were using the ascent autopilot. Did you use any other MechJeb features with your space station?

All engines were turned off, I both throttled down and disabled them, and disabled all RCS ports, Aldo I was facing pro grade which should have raised my apoapsis only. The way my orbit was changing I don't think is possible with the throttle.

I used ascent autopilot, and checked my orbit was stable, then turned my game off. The next day I launched another ship without even controlling the station. Then I realised what was happening

Closing this: it's been a while, I don't think there's much we can do here, and it is probably some sort of physics engine bug rather than anything to do with MJ.