Suspecting something was shorting (no boot, hot components) I decided to check the cable connections to the DB25-contact. Lacking a proper breakout board I connected two DB-25 contacts beginning with just the four power lines (4-5 and 6-7).
Connecting this in line with the cable from the ROV yielded a much happier LED picture on the (naked) controller:
(The second red is blinking)
I'll keep adding leads until the initial symptoms reappear. I'll not attach the (new) BBB until I'm happy that all is well since I've managed to fry the original BBB, However, my local supplier still has 24 in stock......