Update: the animated flash controls seem to be working much better in Fluxbox 1.0.0 from the Intrepid repo. I'm going to do some more testing and try to figure out what to do for Mint 9. For testing I'm using http://www.speedtest.net
and any of the sponsored videos on YouTube.
EDIT: I just packaged a 100% vanilla .deb of Fluxbox 1.1.1 and the problem is still there. I thought for a minute that it may have been one of the patches applied by the Debian maintainer, but it's definitely in Fluxbox itself.
EDIT 2: If anyone wants a 100% vanilla .deb of Fluxbox 1.1.1 then let me know. I have it compiled and (aside from the Flash issue) it works great. It doesn't have a session, so you'll need something like mint-fluxbox-default-settings to get it to work properly.