Those evil gremlins are starting to look pretty suspicious!
DB lock is of course now completely out of the question as is poor disk performance. That I isolated weeks ago.

I don't know about the mechanics of the interaction between Perl and Apache, but is certainly perplexing why (given that it is a network issue) a client could hold back the successful execution of a cgi script. The internet would effectively grind to a halt if that were the case.

I've read that Apache no longer buffers perl output since V1.2, leaving the Perl buffer as the only bottleneck, and like I said, $| = 1; and $| = 0; make no difference!