Is your bike level on the trainer? If you're at an incline in either direction up grade or down grade, I'd imagine it will change the angle you sit. Are you using the same bike on your trainer? If so, that's my guess that it's an angle problem. If you dion't have a block under the front wheel, your body thinks it's going downhill and that could cause a problem.
I know I don't have a trainer, but I'm using a stationary and I don't have a lot of options to adjust the seat right now and I have sit bone and bits issues at times. Good luck.
I know some of the veteran riders can probably help you a bit more, but it's something to check.