It's related to

If XHTML is activated (the default), then forms will be automatically created using [the multipart/form-data] encoding.

Specifically, it doesn't ignore your -enctype => "application/x-www-form-urlencoded" as it should.

Having CGI emit HTML instead of XHTML would allow you to use application/x-www-form-urlencoded. Make sure the MIME type returned by the web server matches the markup language you are using.