Hmm, sounds very, very strange. I can assure you that patrols are supposed to be alive and well in RUb 1.43, if a little reduced compared to default SHIII. They will, in fact, be increased in coastal areas quite a bit in future versions, but in a somewhat different and maybe surprising way
Things like harbor patrols are generally scripted - and none of the scripted patrols have been affected by Ops mod that I know of. So they should be still there, unless you changed the SCR layer, used a non-RUb/Ops one, or it was for some reason corrupted. If you're getting a lot of these unexplainable glitches, I would strongly suggest reinstalling the game and re-downloading RUb.
There's no RUb cities in Scapa Flow, as far as I'm aware. Unless you mean something else, then it's probably one of the default cities.
I can assure you that there's nothing I can possibly think of that would cause graphics glitches like that in RUb. A coincidence maybe? Beery tends to be very thorough with the testing.
As for the 11th - that should be looked into. It's not impossible that the spawn point is off, in which case a hotfix will be on the way soon.