Is this the warning you're getting Wanderer? "Pbank capacity specified for non-ballistic-primary-enabled ship" and then assert failures if you try and fire?
After I switched from a CVS build to the latest trunk from SVN I got that (I'm working around it by tweaking some of the btrl tables since it's not urgent I need them). I'm still learning the code but is it possible this is happening?
In ship/parse_ship at line 3800 the ballistic flag is set (sip->flags |= SIF_BALLISTIC_PRIMARIES;)
Then at 3897 it's reset if a $Flag entry is found (sip->flags = SIF_DEFAULT_VALUE;)