Well, thanks for having a go... "I guess you have a simple wrapper system and have done your own extraction from the sfs files in order to get the required ini and properties files..." Exactly right. And, I'm afraid, that is about the limit of my techincal understanding of the mod. The wrapper/system we use is old-- 10 years, or more. I cannot tell you anything more about it. Sorry to be so unhelpful.
Of course, eveything is/was working just fine according to our current mods. Removing the ShipPack restores this same condition. We have had-- and still do-- one minor curiosity; it has existed for long as I recall in our set-up (I mention here just in case it could be related): armed and moving Chiefs will not appear in the game, although they are placed by the FMB. Unarmed and stationary units do appear. There is no crash/error; they simply do not spawn. Beyond that, I cannot recall any other 'oddities' in our version of the game.
Any road, thanks again for the hard work and thinking about our strange situation. Cheers