are you using mod_perl? OR spawning a perl for each CGI?
resource contention issues in the script for file(s) etc? also, mod_perl or mod_cgi for apache you have to be careful to always re-init all variables and filehandles, as you can end up with values from a different/concurrent web session.
do you want to show us your code?
the hardest line to type correctly is: stty erase ^H