I am using the Logic Compressor effect on my audio and the levels constantly change between uses of FCPX (closing and re-starting). To compound on that even further, I have a duplicated project that is a smaller timeline of the same edit, and it sounds fine, but the original is now about -6dB from what I had originally mixed it to.
Let me say right off the bat, that I'm not sure anything I say here will help you in your situation, but I do 3 edits a weeks and I copy and paste in 3 audio effects to each new edit from a templated project: the Logic Compressor, the Logic Channel EQ, and the Denoiser. I haven't run into what you describe. Two things though:
1. Are you using the built-in Limiter in the Logic Compressor? Not sure this would make any difference at all, but thought I'd ask. Did you notice if the Compressor settings are changing when you restart the program?
2. (This is a stretch, but...) Are you using any other applications that like to re-set a user's audio preferences. I know for a fact that Skype does this and ruined a couple of screen captured class videos I've done this year. This is unlikely the problem in your case because Skype and other silly apps like this will change the system audio levels and certainly not levels within an app.
By the way, I've stayed on FCP 10.0.4 and OS 10.6.8 because everything works for me and through the Cow I know there are some strange bugs in 10.0.8. Again, none of this may be helpful, but I thought I'd chime in because I use the Compressor/Limiter all the time with no problems.