Have you search the unbuntu forums at all about this problem as it seems your not hte only who is suffering this problem. I recommend checking out this topic here and use this google results page to help search for answer and possible post a working result here as well.
Flash Wmode(transparent) Pramater In Firefox3(on Linux) - Not Working
It seems like Ubuntu 8.10 has this issue fixed. I just downloaded the BETA and to my suprise, I have transparent Flash now. Hope that helps.
-reply by Vincent