I've created a demo in Captivate and inserted it into a pptx as a swf. If I view the slide using "shift F5" the swf plays with audio to completion; after publishing, the slide with the swf file transitions after 20 seconds cutting the swf short. I tried creating this slide from scratch but there is no change.
Another issue is that I have slides with annimations timed to my voice. I've recorded the voice and setup the annimation triggers in Presenter. If I play the any given slide from the Presenter Sync window all is well, after publishing, on some slides the annimated elements are all visible at the opening of the slide and there is no annimation, just the recorded voice. And other slides play with the annimation triggers in tact as sync'd.
I am not certain but it seems these issues showed up after running the Presenter 7.0.1 and 7.0.2 updates.