I don't know about SH3, but indeed in SH4 there has to be an empty line at the end of the file, or the last equipment is somehow not read. I already got the habit of leaving that extra line from editing other games that seems to suffer the same problem.
I see in your blog that you keep creating new ships

. Is that the whole line of J-class destroyers and derivatives?. While setting up your line of 30's destroyers for my SH4 I did some reading on the rest of classes, and it was really messy: different guns in ships of the same class, different mounts... It must be a nightmare to model.
Anyway, excellent work. I can't wait to have them

.