i notice a dead spot (a good description) when I get on my geared cargo bike after riding fixed. i think it's a combination of the freewheel and longer cranks (10mm in my case). I had to ride SS on my fixie for a week when my hub was stripped, and I didn't notice it as much. Except of course when I tried to slow down with reverse pressure.
But...hurting spin? I agree with Trevor, sounds like a form problem rather than a mechanical one; or as I say when I'm wearing my IT hat, an "end user error."