I have heard that if you live/work in Spain for a prolonged amount of time, there is a cap on the number of times you can fly back to the US and a waiting period to return (even if just going back to visit). Anyone heard of this?

I have heard of this, and I do believe you must have a special, independent-type visa which would allow you to travel back and forth (what do traveling salesmen do???). But I am not sure. Will research it for you and get back to you
If you don't feel like waiting for my response, ask at the Spanish embassy in USA or the American Embassy in Spain.