How are you inserting the flash? Are you using the insert flash dialog in the editor or just copying and pasting code into the editor?
I tried just copying and pasting into the code view of the editor using this code and it appeared to work fine:
<EMBED src="animation/transparency.swf" wmode="transparent" quality=low bgcolor=#99CC00 WIDTH="300" HEIGHT="200" NAME="transparency" ALIGN=""
What does the code to embed your flash look like?