By the way, it flashes with a black background.
Does this happen with a specific SWF file or any imported SWF?
Can you tell us the build of Presenter you are working on? Once you go to Presenter tab inside PowerPoint, look for "Help" and click "About Presenter".
kindly tell us the build number mentioned there.
If the issue is happening with a specific file, please share the SWF ifle with us at firstname.lastname@example.org
If you are using 7.0.6 or older, then you should be using an AS2 SWF, as you are, and I would reccomend working with Mukul to find the resolution. If you are using 7.0.7, then the SWF is likely the issue as this version uses AS3.