From what I remember are GUIs connected via a socket connection to the normal Perl debugger.

The actions are just translated into normal debugger commands.

That's at least how IDEs like Emacs connect to the debugging process and like tye already said debugging threaded programs should be supported by normal debugging.

So If I were you I'd try to replicate the problem with the plain debugger ( perl -d ) and then an IDE like Komodo or Emacs.

If these work, then the problem is most likely on the client side.