That is the pain of low-level recording. Unfortunately, you are very vulnerable to application changes and how it impacts your recordings. Even resolutions will impact your scripts - if you recorded on a 19" screen under xx resolution and run it again on a 24" monitor with yy resolution - it likely will not have the same x,y locations.
Below is a good article on the topic for alternatives for testing of Flash. I can't guarantee success, but it might point you in a good direction.