I think I figured out what was wrong. I disabled add-ons and deleted some things off my computer and even installed. Microsoft DRM is still disabled in add-ons, so are; Pando Web Installer, Windows Media Player Plug-in Dynamic Link Library, Windows Presentation Foundation. I uninstalled programs that came with my FIOS that were not needed. I also got prompted that I had a DIVX update which I have been putting off for a while. I would always click remind me later but after I decided to install it, my videos no longer freeze.

This bug still exists as of beta 13/nightly 15. When watching Flash videos, occasionally the browser will freeze up and go unresponsive for about 5 seconds. Audio continues playing and video resumes in sync afterwards. Happens with HTML5 player and Flash, suggesting it's not a system codec problem. Does not occur in any other web browsers either, watching videos on the same sites.

This problem was affecting me in Firefox 12 as well.

I solved this by uninstalling flash, and reinstalling the 32-bit-only version of the plugin.

Get the 64-bit flash uninstaller here: http://helpx.adobe.com/flash-player/kb/uninstall-flash-player-windows.html

Get the 32-bit flash installer here: http://get.adobe.com/flashplayer/otherversions/

Edit: The separate 32/64 bit versions of the uninstaller/uninstaller were removed, but the issue seems to have been resolved in the current version of the flash plugin.

I did the Flash uninstall of 64 bit and re-install of 32 bit and it didn't help, but so far I found 2 things that can help! If you have SEOQuake on your browser, disable it, then watch a video! This fixed the video problem for me (so far, so good anyway)! (You can enable it again anytime).

If that doesn't work, try clicking Firefox, Help, Re-Start with Add-ons Disabled. (Puts FF in Safe mode - just the browser, not Windows too). Watch a video now - if it's OK it means one of your add-ons is the problem. Close FF, then re-start it (it will start normally with your add-ons enabled). Click Firefox, Add-Ons. Disable one of the add-ons, then watch a video. If the video still freezes, that means that one wasn't the problem. Try disabling a different one, then watch a video, etc. till you find which one was the problem!