I don't see how the dongle could cause any problems. It's never being "disconnected" from the keyboard/mouse, because it's hooked up to the KVM. The individual computers are being disconnected/connected to a degree, but all modern KVM switches emulate a keyboard/mouse being plugged into the comp but not sending any input signals.
It should work fine. Now, as to your original question, I'm using an old D-Link KVM switch (2 port - can't remember the name). It works well, but is analog only. I really want to get a good DVI KVM switch (bought a Startech 4-prot one a while back, but it had problems with my setup and I ended up selling on ebay for a loss).