Hey Gazz,
Not sure if this falls under your list or not, but some of the ships have their turrets, how should I put it, misassociated?

Look at the gun mappings Galleon. As far as gun positions being the "same", the "Right" and "Up" can pack the same guns, and the "Left and "Down" have the same layouts. I'm betting the "Left" and "Up" should be switched so the R/L and U/D match. See what I mean?
I'm betting the Galleon is far from the only ship like this, but seeing as though I have 4 in my fleet, it was the first one I checked.

I imagine this change is probably in TShips or something but since I haven't bothered to dig into it and figure out the format of that file I figured I'd mention it here. ;P