I think I've progressed in my analysis. I noticed that the MapUpdates "un"mod doesn't copy back the source submarine *_shp.tga files, which the RUb readme says are also changed as part of the realistic plotting mod. Guess what...copied them back and no more black box.
So, this appears to be the solution if you are running the MapUpdates "un"mod. If you're not running the MapUpdates "un"mod, then I reckon there is a problem with the submarine *_shp.tga files included with RUb. Maybe a transparency setting? Maybe a combination of the files and our video cards/drivers? I dunno, so I'll leave this to the graphics experts to comment on...