Simon Baxter sent me a similar report, but with debug code inserted which showed that cVideoRepacker wasn't completely stuck.
Is it easy for you to trigger this issue? I've tried two simultanuous timers plus watching a recording but couldn't trigger the issue.
Please add the following 4 lines, which are marked with "<========" to the appropriate source locations (cRepacker::Put(), cVideoRepacker::Repack()) in remux.c and send me the output when the problem happens again.