Are you trying to use the "automatic reload" of changed modules - Apache::Reload or Apache::StatINC or something similiar. If so I think you need to make sure that the directory is in @INC (I can see /apache/lib/perl but I don't know if that is what you are using). Perhaps you could reply and let us know what you have added to httpd.conf to get mod_perl working.
Comment on Re: mod_perl losing/confusing file paths?
This looks o.k. but is your perl directory in @INC? if not you can add it in the startup script (startup.pl) use lib qw(/home/httpd/perl); # for example
I don't really know why this works but it did for me. Also you can start up Apache with a single server process -XI think which would be worth trying to see if you still get the problem.