handler() is the name of the sub that mod_perl automatically calls if you tell it to use your module as a content handler and are not using something else like Apache::Registry. Are you trying to use Apache::Registry? Do you have a handler sub in your module?
Im not using Apache::Registry since this is mod_perl only and yes I have a handler subroutine, as I say this fault is intermittant so while 99% of the time it works perfectly the other 1% it 500's :(