Do you have a different saddle tilt on the trainer than on the road?
The thing that holds my front wheel tilts my bike up a bit so I usually re-level my saddle when I put it in the trainer. I also adjust the angle when I am ready to take it out on the road.



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My previous saddle dug into me a bit when tilted up so I would adjust the saddle tilt... 
It's not very high but I was wondering if it was unusual that I change the seat tilt slightly when I'm on the trainer 