It could mean it's never executed. That could be due to path issues with the perl program (unlikely, since it works up to that point). It could be due to child program limits or the web server user's process limit. It could be due to a memory limit on the web server process and its children or the web server user. It could mean something, somewhere, is causing a syntax error (unlikely, since it works initially).
If it happens around the same time of day, it could be due to time range issues in your ACLs (which is also unlikely, since you say restarting the server works no matter when it happens).
It could mean the CGI program is running but unable to open a file handle for its STDIN to get info from the server or STDOUT to get information back to the server due to file handle limits.
It's a good idea to know about how many file handles the web server user has open, how much memory all the processes it runs are using, and how many processes it has running when this happens. Then, compare that to the mechanism which limits those things. It's ulimit on Unixy systems; I don't remember the name of the policy mechanism that handles such things on Windows.
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