Since you can run the script in the main /cgi-bin directory, I assume you haven't made mistakes like uploading as binary instead of ASCII, ignoring case-sensitivite filenames, or anything like that.

Do you have access to your server error logs? That might be the easiest way to get an idea what's going wrong.

If not, I would start by trying to figure out whether the problem is indeed in your server config/permissions or somewhere in your script. (Seems unlikely that the script would fail simply because you changed directories, but without code I can't be sure what assumptions your program might make.) Anyway, you could write an extremely trivial cgi script -- like "hello, world" -- and see if you can get that to run within a directory under cgi-bin. If so, you could put use CGI::Carp qw(fatalsToBrowser) near the beginning of your script and probably get a better idea where the failure is occurring.

I suppose it's possible that Apache is configured to execute scripts only within cgi-bin, though if that's the case I'm surprised that you would've been able to use this technique in the past.

        $perlmonks{seattlejohn} = 'John Clyman';