I have a project that I am using cue points. I have several in each video. The first works fine. The second and third do not recognize cue points i labled "end". I have gone through and removed the other cue points and kept only the "end" cue point. It still lists the first cue point even though it has been removed.
Are the cue points actually embedded in the video? or added via actionscript?
There are two parts to cue points... the cue point itself either embedded directly into the video or detailed via actionscript and then there is the "action" that the cue triggers.
If all you are doing is removing the "action" (event listener or whatever) but not the cue point you would see a situation very similar to what you describe.
Best to post the code used to create the cue points, the listeners, etc, and then describe in detail how cue points were first added and the later removed. So we need more details to better diagnose.