When under a mod_perl environment, the directory that the perl script is started in can differ from the directory in which the script file itself is located. I'm not sure if it is always the case, but my mod_perl starts scripts up from the apache root (So in my case C:/Apache2/www/port80/serve/foo.pl is executed as though it were C:/Apache2/foo.pl). The simplest way to make it back to regular CGI behaviour is to change directory from within perl. So at the top of your script, you just throw in this line:

BEGIN { chdir "/path/to/script/directory" }
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My foo.pl script as mentioned above for example, would include this line:

BEGIN { chdir "C:/Apache2/www/port80/serve" }
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That's only the case with mod_perl 2. In mod_perl 1, Apache::Registry does the chdir automatically.

I'll remember that in case I ever have to suffer the long journey of porting anything from mod_perl 1.x to mod_perl 1.9x/2.x. That would certainly be a strange thing to see happen if you're not expecting it. :)