I've run into this problem as well but I found a simple fix that seems to work.
For me it was happening only on computers that had Firefox (I have 2.0.0.8), Quicktime 7.2,
and an nVidia video card, though others seem to have slightly varied results.
Changing Quicktime preferences (Enable Flash, MIME or File Type settings) does not resolve the issue. I've tried changing nVidia driver versions (163.44, 163.75 beta) to no avail. I'm now back to the current forceware release 163.71 from nvidia.com.
Uninstalling QuickTime completely fixes the issue, but then you don't have Quicktime, which is not an unacceptable fix.
What DID fix the issue was this (steps 3 and 4 may not be necessary for everyone):
1. Uninstall Quicktime 7.2
2. Install Quicktime version 7.1.6:
http://filehippo.com/downloadquicktimeplayer/?2607
3. Re-install Flash Player:
http://www.adobe.com/shockwave/download/download.cgi?P1ProdVersion=ShockwaveFlash
4. Restart the computer.
Flash objects will now display normally, and the "Q" icon with the question mark "?" will no longer occur on sites like youtube.com, last.fm, and so on.
Edit:
I know this doesn't resolve the issue with Quicktime 7.2, but as far asI can tell from my research, there is no actual fix for this issue that includes keeping Quicktime 7.2. If there is, I'd love to read it.
As of now, my best guess remains that this is a bug in Quicktime 7.2.
Please let me know if this fix works for you or if you've found other fixes.