That looks like the dial faces or needles lost their transparency, but the depth one didn't?... did you happen to check the dials in the Control Room? the Conning Tower interior? I have not ever seen that, but then again, there is a lot about this game that I have not seen...
- Was this Save from a previous game state, such as having one of the test mods installed previously, and then removed when you re-loaded the save?