Except for the details of your app (the gpg stuff), this is a FAQ:
My CGI script runs from the command line but not the browser.

The FAQ entry itself doesn't give any direct answers, but it does refer you to the "CGI_MetaFAQ", which includes a "Troubleshooting_CGI" document.

Unfortunately, the URLs given in perlfaq9 don't seem to work (at the moment), but if you know that brian d foy is the maintainer of the CGI_MetaFAQ, you'd eventually find it in his sourceforge area.