If you have your AirPort Extreme connected to another router......the Extreme should be running in Bridge Mode, not Router Mode.
Otherwise, you have two routers on the same network both trying to run things. This also produces a Double NAT error, which slows the connection down on most networks.
My guess would be that the new firmware update sensed that the Extreme needed to be in Bridge Mode and configured it accordingly. Unfortunately, the Guest Network is not enabled when the Extreme is configured in Bridge Mode. Kind of a Catch 22 there.
I would expect the Time Capsule to try to configure itself correctly on the network, so you will likely face the same "issue" with a Time Capsule.