Apparently... the game doesn't detect files by their name... and all the times I repacked the bloody Main.pak, while keeping decidedly renamed backup of main.pak - the game loaded my backup and drove me nuts.
As Baardvark said, you don't really need to repack those files to work. If you do repack though, keep in mind that the game loads packages in alphabetical order, and "newer" stuff overwrites "older" stuff.
So if you replace one of the LSX's in A.pak, then it'll probably get overridden by Main.pak because it is loaded after your pak. If you don't want the game to load a package, just rename it to Main.xxx or something other than .pak
AFAIK packages in the Mods folder are loaded after packages in the game Data folder, so putting them in Mods should be fine.
