Windows 2003 Server is super strict with any program run under it. If it detects a buffer overflow in the code it will kill the application immediately without a GPF, the process just disappears. Perhaps something in Perl or the MySQL driver is causing an issue.
Have you tried on a Windows 2000 machine?
Update:
Here is an except from Changes to Functionality in Microsoft Windows XP Service Pack 2 which is basically what MS is doing in Windows 2003 Server.

Memory protection. Some attacks by malicious software leverage software security vulnerabilities that allow too much data to be copied into areas of the computer’s memory. These vulnerabilities are typically referred to as buffer overruns. Although no single technique can completely eliminate this type of vulnerability, Microsoft is employing a number of security technologies to mitigate these attacks from different angles. First, core Windows components have been recompiled with the most recent version of our compiler technology, which provides added protection against buffer overruns. Additionally, Microsoft is working with microprocessor companies to help Windows support hardware-enforced data execution prevention (DEP) on microprocessors that contain the feature. Data execution prevention uses the CPU to mark all memory locations in an application as non-executable, unless the location explicitly contains executable code. This way, when an attacking worm or virus inserts program code into a portion of memory marked for data only, an application or Windows component will not run it.

In reply to Re^5: connecting to Mysql from Win32 by terra incognita
in thread connecting to Mysql from Win32 by bfdi533

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