It is not a VM, and it is Aolserver 3.4.2. I'm betting that it will turn out to be something simple like that, but it isn't the stacksize, or at least I haven't changed the stacksize.
To make the copy, I just copied /web/server1 to /web/server2, and made the few necessary changes to the server2 config file. Both servers are for the moment using the same database, but I wouldn't expect that to cause this kind of trouble.