I'm no expert, but it doesn't seem to make any sense from the programming aspect of the program since they are all running on the same machine. If the program passes commands to a portion of the clients, you know that the program is working, so I would guess it's a Vista issue, perhaps even something to do with the 64 bit variant.

How are you starting the other windows? I would try various methods, but ensure that the UAC isn't causing problems of some sort. Try running the windows that aren't responding by themselves, one at a time and see if they ever respond.

You gotta love computers.