MiGBuster yes it is in Single mission mode, I haven't test campaigns yet. The default loadout is Aim-9Ds, Fueltanks and LAU-3 etc.
What type of mission are you selecting? That shouldn't be the default loadout for any mission in an A-6.
Also, like someone mentioned, NATO fighters and the weps pack don't really work well together, since NATO fighters installs it's own weapons. I would try reinstalling everything (yeah, that sucks) and don't add NATO fighters, or maybe just install WOV and don't merge with WOE, and see if the problem goes away.
If it does, go ahead and merge with WOE and install the weps pack if you want, but don't install NATO fighters. Do a separate install of WOE for that if you want it, or go to
http://www.combatace.com and you can find pretty much all the planes for NATO fighters and install them separately without messing with the weps anymore.
Good luck!