You might want to try invoking something other than perl from the #!, like /bin/bash. If #! /bin/bash also does nothing, there's something wrong with your shell/os/something-other-than-perl. If you get a bunch of bash errors, that means bash did try to interpret it, so the problem is probably perl specific.

Also, erasing and re-writing the #! line will remove any of the line ending/other invisible character weirdness possibilities.

Did you copy the working script ( /var/www/html/hello.pl ) over the wierd one ( /var/www/bugs/hello.pl ) or did you write them separately? Make sure they're absolutely identical.

Last idea, this one is a TOTAL long shot. Is /var/www/bugs a different mount point with execution restrictions?