Ok, I have gotten to the bottom of this problem.
The way the ASTAC interface determines loadout is based on the mission priorities set for each assigned weapon in the database.
If the weapon has ASuW assigned as one of its mission priorities, and it is assigned to any of the launchers on the helo, then it will show up as listed under ASuW.
So, the fix, on the interface side of things is as simple as changing the mission priorities back to ASW only for the MK54II (which is only on the MH60 so it shouldn't effect anything) and Strike only for the Hellfire Strike (this is again only on the MH60 and I can still enable human fire on ships, so I think this can be corrected without consequence).
So basically, I have fixed it. It's just a matter of when you guys want me to release the fix... I did have some doctrine tuning I wanted to do, perhaps I can release an update in the next couple days.
I'm going to start an "open issues thread" so I can get rid of any of these little ones all at once.
Thanks again TLAM for bringing this up.