Perhaps they weren't strapped down tightly enough, and the pounding at high speeds (anything above 6 knots in my case) might have caused them to move and bounce within the boxes?
It's a scary thought having loose acid in the hull, with seacocks, anode bolts etc straight through to seawater. Glad you found it early!
Frisky has 2 domestic batteries (11-12 years old but getting tired) and 1 cranking battery (second season), all 110 amp hour and about 12.8v at rest, with switching available. I don't have boxes, but have all batteries strapped down tight to the hull webbing, in the event of a knockdown. I do like the idea of boxes, and will investigate if they might fit!
Mike