If you want good answers, you might wish to take the advice offered here.

Aside from that, at a glance, you don't use strict, you are using cgi-lib.pl rather than CGI, your temp file handling has a ton of race conditions, your lock file handling means that if anything went wrong it would tend to randomly fall over.

I don't know what specifically causes the (unspecified) symptoms that lead you to post, nor do I feel inclined to dig into it deeply enough to figure that out...