You may have to get someone with some masonry background to take a look....friend of mine just went through the same thing in his living room and they had to use the "blend in" approach. I could tell and it would bother me....he had two guys come look at it with both giving the same explanation...
Had the same problem and did treadmill work after a month layoff to build back muscles/conditioning. It worked like a charm. Try treadmill and run pain free, after a a month or so you can hit the roads again.