As we've never experienced it ourselves, it's very hard to track down what it might be, and even that, it's very likely a Janus problem, the menus are janus controls. I can find 1 description in their changelog which might be the fix of this, though I'm not sure.
The main problem is: I can only download the latest build, which is v3.5, not v3.0. This means that if I download v3.5, users have to upgrade both the designer AND template studio at the same time.... and history learns that that's a pain.
It happens every time? If you run it in vista with the 'xp' compatibility mode, does it work then?