Mike. am I hearing you correctly? When you use a PC Preset (Fingered Bass, for example), it gets inserted in different configurations in different tracks? Like, EQ off in one, Compressor off in another?
I happen to use Fingered Bass PC Preset very often. It loads the same way, every time, every track. I use it as a starting point, and tweak to taste. It behaved this way in X1 and now in X2. Actually I use quite a few of the PC Presets, and have never seen the phenomenon I think you are describing.
So I am at a loss for advice to give you.
BTW- there are quite a few very useable, musical PC Presets if you give them a try. Take a listen to "Electric Dirtbag" on a crunch guitar track, or "Concrete Kick" on a drum track. You might like them.
Hope you find the problem and share solution.