did your PT teach you how to relax/adjust your own sacro-iliac joint? If that goes out of whack it will cause the pain you describe and also give you a functional (though not anatomical) leg length discrepancy. Now would be a good time to do any of the alignment techniques they taught you.
Can you call the PT and tell them what you're feeling and ask them for some advice?
Are you still doing the exercises and stretches from your home program every day?
Are you stabilizing with your abs on the bike, just like you do the rest of the time?
"If Americans want to live the American Dream, they should go to Denmark." - Richard Wilkinson