You are right: if the GPS is blocked it should still shut down.

I would try testing your unit on someone else’s boat that is running a Humminbird unit. It does not have to be another 597ci unit. This can be tested on land as all you are looking for is the GPS to work (or not) and for the unit to shut down correctly. Make sure that the other boat is out in the open so that the GPS Receiver can get the signal from the GPS satellites.

If the GPS works on the other boat you will need to either relocate your unit or the rod holders.

If the unit shuts down correctly on the other boat, you will need to check your wiring. All connections should be soldered and sealed. Check for any loose or corroded connections – even in the fuse holder and the fuse. Ideally you have the 598’s power cable connected to a set of wires that runs directly back to the cranking battery of the boat (through a blade-type fuse and fuse holder). Low power can cause some funny things to happen, like the GPS not working and the unit not shutting down properly among other things.