However, I'm beginning to suspect that occasionally (maybe when the web server is busy) the flock call fails.
If you're unable to show us code (or even if you are), it sounds like this calls for a basic debugging technique: strip extraneous stuff out, and see if you can come up with a small example that demonstrates the problem. Quite often, the act of removing stuff that you think isn't part of the problem either reveals that some of it really is. Or, the real problem is laid bare.
Since you're working with CGIs, that might mean figuring out some way of programmatically driving the web server (e.g., by multiple LWP clients).
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