Hey Chris, are you using a dummy object for your player character? (That is a base object with your character pinned to it).
Collisions can be different for each frame in an animation (you have complete control over that - there is a button in the image editor that shows what the collisions look like). To make it simple you can base collisions on the dummy object instead.
I'm sure there are tutorials but if you post a simplified capx it will be easiest to help.