Okay;
5549, bombers launch 4 bombs on their way into the Ptah-Nu at the start of Apocalypse.
5550, bombers launch 12 bombs on their way into the Ptah-Nu at the start of Apocalypse.
It's _definitely_ 5550 
And I assume you still get the 12-bomb thing in the latest nightlies...
5550 is a fairly small commit by Kara, with the following changes:
Change #1: Fix afterburner bug.
Change #2: Remove unreachable code.
Change #3: Added some missing typecasts dealing with ships taking off or landing at a hangar bay.
None of those things seem like they should have any impact at all on bombs. Very strange. To be honest, I haven't a clue what's going on there.
Maybe there's some other subtle difference between nightly builds the builds I've been giving you? Here's a 5550 that I built, if you want to check:
http://www.mediafire.com/?sharekey=767261bd3368c539b64026cfc0611236e04e75f6e8ebb871Maybe that 'unreachable' code wasn't so unreachable after all?
Maybe, but I don't see how. It's of the form
if (Stuff)
{
do stuff
return
}
else
{
do other stuff
return
}
unreachable code here
Seems pretty unreachable to me...
EDIT: Besides, that code has to do with primary weapons, not secondaries.