I have the same problem even with a mouse, and it happens with lots of flash video providers too. My trick is just to click somewhere else on the screen and continue scrolling. Apparently after scrolling past an active flash video, Chrome gives it focus so any scrolling you do more "affects" the video rather than the page...
Very annoying. I'd suggest you send a bug report to Google. They're pretty good at keeping up with these things, and the more of us who whine a bit the better they'll respond. ;D