I'm only using a few mods that are handled with Jsgme. Before updating to 1.2, I backed out the mods, installed 1.2, then activated the mods again through Jsgme. The Battle Station and Silent running mod to all icons is great

My previous saved career wouldn't load, so I started a new one.
Added Berrys new Fleetboat mod through Jsgme too. Since it has the green light mod built in, I backed out the single mod.
I haven't changed any files manually, but I need to find a way to fix that southern heading radar bug. The boat just can't get down fast enough when an aircraft is spotted visually
If the save games are still buggy, I recall that all the way back to SH2. Must be some root code that UBI is still using.