I'm having the exact same issue that's being described. Any breakthroughs for anyone? I'm not running HD, and I don't have CPTK, so cutting the video isn't an option for me. I really don't want to have to change my workflow if I don't have to.
Edit: Found the issue. "At a certain point during playback, an H.264 video file over 2GB in size will incorrectly restart playback from the beginning, even though the timeline indicates it is not playing from the beginning. The workaround is to place an edit (break) in the video clip prior to the point it starts playing incorrectly from the beginning. This issue only affects H.264 files larger than 2GB." from
http://akmedia.digidesign.com/suppor..._Mac_78009.pdf
Sorry! Should have searched for longer. Still an annoying bug though. So this is still a problem in 11?