So i'm merging mods - effectively ammo/weapon mods into a cohesive (unbugged) collection.

What I've noticed is a weapon (any weapon, they all appear to work this way) can have an ammo list as a reference for ammo type, and the ammo list can have a list of ammos, and the ammos exist - for sure - but then in game the weapon can not use those ammo types. I can even add them to my inventory using the console, but the weapon 'ignores' them as being legal.

Case in point: the Jackhammer Pancour from the 20th Century weapons mod ignores all other 12 gauge rounds except for the vanilla one ... even though other 12 gauge rounds are in the 12 gauge list.

The Cowboy Repeater (vanilla gun) ignores a CALIBR ammo .357 ammo type, even though that ammo type is in the 357 list.

I've turned off all other mods, I've confirmed that the ammo types are in lists, that the lists are referenced correctly from the guns ... but in all instances the ammo does not turn up as being available.

Should I be recompiling the .esms or anything 'special'? I'm pretty darn sure at this point that no conflicts occurring (after painstaking checking and merging), so why is the GECK showing x-amount of ammo types in an ammo list, and yet the gun that references that list can only use 1 or 2 and ignores the others?

Never had any problems with it. Are you editing the correct formlists?

AmmoList357Magnum for example.

Yes, pretty sure. Under form lists, right? I have followed the instructions on the geck wiki, but new ammo type is not showing up as valid.

Is it flagged as playable?
Also, I think Pintocat's referring to the way there's multiple ammo lists for some ammo types- so you may be fixing one of the .357 lists, but it might not be the one your gun is using. The Jackhammer you mention also sounds like it's just using a single ammo, rather than an ammo list.