Just reading your post over but one thing that jumped out is you can disable and enable collisions pretty easily. It would get around the problem but if you want to post a link to your file I'll happily take a look at it. :)
I had a problem like this on my game where a barrier was slowly destroyed by aliens. The problem was that the collision was happening again and again.
It was caused by different animations having different polygon collision shapes. Have you checked those?