Ah I figured it out. It wasn't the mod, it was my trying to use the mod with a saved career PRE-mod installation!
I've started over again, sailing out of Kiel in a shiny new VIIB...and Kaleun Bernhard Locker (as in, "...to the bottom of Davey Jones's...") in command. I have barely sailed out of port and ALREADY love the improved interface and dark atmosphere! This mod makes SHIII even better, and that's no mean feat!
Thanks for the suggestions all. Now off to sink some limey tonnage!