Does anyone find that putting your bike on a trainer affects postioning? I can do century rides outside with no pain - meaning no injury pain, still have muscle fatigue 
Put the bike on my CT and after 15 minutes I have lower ab/groin type pain on one side, slightly above the crease between your leg and groin area. Anyone else deal with this?
my position is definitely different. For one, the trainer forces your bike into a certain position that in my case is not completely vertical or level due to slight variations in ground elevation and the cheapness of my trainer. This causes me to sit a little differently on the bike than when not on the trainer. Outside, I achieve an equilibrium naturally that keeps me from falling over, and gives me a more symmetric position on the bike.
Maybe you are experiencing the same thing.
I gave up on riding the trainer. It sucks for alot of reasons, one being the change in your position .You have to use your muscles differently IMO. No proof of course, just what I think