You don't give enough detail to tell what they problem is. From experience, I do feel that powering the bike on a trainer is very different than doing it on the road. It seems to burn up the quads way more (less hamstrings & glutes) and you are not using much of your core and hip stabilizers. Having said that, perhaps it has something to do with your hip adductors or some other core muscles that support the low back. You don't need them much on the trainer like you do on the road. Once again, I don't know what areas on you feel like crap.

Nick Z
Bought A Bike Online? I Come To You Build & Fit It. Road Mountain Tri