frozen windows

I'm experiencing a really weird bug where certain windows won't accept any 
input.

C++ binary --> perl script (via "system") --> gdialog (via "system")

I end up with a gdialog window popping up, but it will not accept any 
input, and I can't change to other windows via alt-Tab.  The default 
button in gdialog usually has a dotted box inside it, but that never 
happens.

It gets even weirder, because sometimes it works fine.

Calling the perl script from a terminal always works fine.

Xdialog, or even xterm, have the same problem.

This seems to be a wm issue, because it works with twm (so far).

Any ideas?


Thanks.