For what it's worth, I always have my audio slide by slide, not spread over slides, and I never have problems with the synchronisation. My slides are rarely more than a minute in duration.
You can chop up the audio inside Captivate using the method you mentioned. Or, if you have the ELS suite then you have the option of exporting the audio files from Captivate and using Adobe Audition to select segments to save out as new audio clips. Either way is going to be a pain this time around.