I had the same experience when I switched to spinning from running due to an injury in my foot. The first time was not good, but significantly better the second time and now it doesn't bother me at all. Spin bikes are great in that you can adjust the seat (up/down and forward/back) and handlebars up/down.
The staionary bikes at my gym don't offer the same flexibility in adjusting so I use the recumbant bike when I work out on my own.
For me, spin has been a great substitute for running. It gets my calorie burn and HR up to what it is when I run and it is non-impact. For example, last night at my hour spin class (including warm up/cool down and a few minutes of stretching) I burned 632 calories.
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