How was Emacs configured and built on your platform?  What's your platform?

Can you run the shell command 'strace -p' on an Emacs with the problem, 
and trace the system calls near the offending area?

Are you using anything involving SIGUSR1 or SIGUSR2?  I see an unlikely 
race condition there.

That's part of the problem with this code: it's so racy that it seems 
that every time I look at it I find another unlikely race condition. 
I'm attaching a patch to emacs-24 for the unlikely races I found in a 
quick look at the area, not that I think it'll fix your problem.  I 
haven't installed this.