As Inada-san indicated, the problem might be resolved already.  So without the option of reproducing the problem, it will be hard to resolve this.

Here's some information you could provide that might help narrow down the scope a bit:

* what (stdlib/third-party/internal) modules are you using, particularly extension modules?
* how many threads are you using at once?
* how many atexit handlers do you have and what are they each doing?