Falkhor:
Windows, Chrome.
I had the problem before, then for a while it was properly aligned. I think with a recent site update the issue may have returned.
I investigated this on a game I don't run, and I found that I didn't have complete functionality, so I checked with one I do run. I'm not having the problem on W7 with Chrome. You may need to go into Hardware and Sound (or whatever yours is if you're not running W7) and adjust your mouse sensitivity down. Sorry if you've already tried that. I was having a similar problem when I was stuck on a tablet. I don't know if it ever got resolved, because I no longer require my tablet.