This may be an Apache thing, not a Perl thing (or at least related to the way the two work together). I find I can successfully run this script from the command line:
system('notepad');

So apparently the GUI itself isn't a problem. Then again, if I try to run this script via Apache, it hangs as you described.

A search in Google's Usenet archive turned up old threads (from 1999) about this, and indicate that it occurs for PHP scripts as well as Perl. I didn't see any obvious solutions, but I didn't check every thread either ;-)