Make sure your SWF is an AS3 SWF and not an AS2 SWF. Flash objects in AS2 or older won't work in Presenter.
Instructions for inserting SWF content in Presenter: Presenter Help | Importing SWF files and video files
It is an AS3 SWF. Funny I can get it to play in Captivate although with lesser glitches still there that can be worked around in Flash. But these SWFs just plain break inside of Presenter. Hopefully I can get some explanation to what is happening and try to fix or unfortunately I'll have to rebuild my presentation using another tool. So much for the marketing hype that sells these products but deliver less than advertised.