OK 2DarkWolf2, a few preliminaries: Did you empty the Save folder before playing FotRSU? Do you have the game installed in a non-Program Files folder? Do you have LAA (or similar) properly enabled on the SH4.exe file? Have you done any mod adding or deleting between Saves? When you Save, are you using unique names each time? Do not save on top of the previous Save.
Now, FotRSU is based upon TMO v1.7, so it has the same set-up to where your submarine is visible beneath the surface, at depths up to roughly 160 feet. This also depends upon how "high" in altitude a plane over-flies your location. Generally speaking, you should be fine cruising around at 120 foot depth - usually. There are ASW airplanes constantly on patrol, such as the H6K, H8K, Lorna, and especialy Betty & Judy that can all carry regular bombs, as well as depth charges. Second of all, there are minefields out there, especially in Empire Waters. Here is a portion of the file that holds them:
There are more north of there, more south of there, more off of Formosa, off of Korea, in the Korean Strait, Tsushima Strait, Tsugaru Strait, etc... So you can indeed run into mines. Let us know though, where you were Lat / Long wise, and we'll see what we can see in the area. As another note, airplanes will usually fly over your last-known location twice. In 1944, it might be radar, and if it is, and it is something like a Betty or bigger, they will drop a couple of bombs near you last radar location, then come back and do a couple of more, further along your last-known travel line, and if they still have bombs left, might do a 3rd pass. If the plane used HF/DF to zero-in on your location, then they may not drop bombs the first pass. But if they saw you, they will drop and drop until they run out, then they'll call their buddies to come get ya...