Check to see if Time Machine is backing up your system when you stop the recording.
Okay so I was having the same issue with QuickTime screen recordings and even lost a very valuable Skype interview due to the bug. Eventually I figured out what was happening. When I clicked stop recording and the new video didn't appear and the option to quit QuickTime grayed out I was invariably backing up my system with Time Machine. I have Time Machine set up to automatically back up my computer at regular intervals so I was not doing this intentionally, it was just a bad convergence of events. The first time I tested my theory out by just letting Time Machine finish it's thing and, voila, the video popped up as soon as Time Machine finished its back-up. The second time I tested it out by just clicking on the Time Machine icon and forcing the back-up to stop. The video instantly popped up when I stopped Time Machine. Most importantly the video and audio were both intact! This is not what happened with my Skype interview which I impatiently tried to grab from the temporary folder not realizing the hang up was due to Time Machine. When I moved the temporary file QuickTime could no longer find the file once TimeMachine stopped. I didn't notice this right away because I left my computer for a couple hours thinking the video was irretrievable. When I came back to my computer I had the error messages and the video worked but not the audio (the whole point of the interview). So goes it. I am glad to have noticed the Time Machine problem and hope it helps others.