I usually only ride the trainer for recovery rides, and I didn't feel like riding at night in the rain so I decided to do intervals on it for the first time and I actually got the same feeling. I woke up today with sore hamstrings. I also got that feeling you get when you hop off a treadmill, as if you're floating, for the first time. I think that it does tend to work out other muscles you normally don't use or use as much then you normally would when out on the road. But still works out your quads, calfs, etc.