This thread has some relevant background, though it doesn't look like there's a solution. I found it in perlbug as well, it's a Windows 2003 specific bug, and appears to still be an open issue.

Update: Perhaps the alarm() or ualarm() functions in Time::HiRes will allow you to work around the issue?

In reply to Re: alarm not triggering SIGALRM on Windows 2003 by thunders
in thread alarm not triggering SIGALRM on Windows 2003 by perlofwisdom

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