After doing some additional tests, it appears that only certain items save state properly for the instance.
The following ARE set back to the way they were (ie works properly) when I closed the flight and reloaded it:
Battery and Alt Switches
Fuel Pump Switch
Landing Light Switch
Anti Collision Light Switch
Pitot Heat
Avionics Master Switch
Transponder state switch - Off, Stby, On, Alt, Tst
Fan Speed - Hi, Off, Low
The following are NOT saving and are reverting back to their default:
Transponder Code - It resets to 7000 normally, but sometimes 2000 or 7004, which is odd.
Throttle - It would reset to fully closed (ie fully down)
Mixture - It would reset to cutoff (ie fully down)
Parking Brake Switch - It resets to ON
Carb Heat Switch - It resets to OFF
Comm 1 and Comm 2 Frequency - Each resets to 124.850 for both active and standby.
Nav 1 and Nav 2 Frequency - Each resets to 110.50 (Active) and 113.90 (Standby)
Altimeter Setting
Nav/GPS switch next to the Nav 2 VOR
Note 1: If it wasn't listed above as saving or not saving, I didn't test to see if its state saved or not.
Note 2: During each test I am using the save livery / tail number.
Note 3: It appears using End Flight or Main Menu to exit out of the active flight works when restarting. I also tested exiting out of MSFS 2024 and reloading, and it appeared to work but I didn't test multiple state changes for that.
The aircraft is setup as follows in the EFB:
Auto Fuel Selector - Disabled (Black background)
GPS: WT GNS DUAL - Enabled (Light gray background)
State Saving - Enabled (Light gray background)
HSI - Enabled (Black background)