It seems whenever I start a new character, I cannot see "Mod Configuration" in the pause menu and have to de-activate and re-activate PN in the mod manager. It seems to have something to do with the hud menus file. I use the combined hud project thing as well. Any reason why this could be happening?

I just found out that I still have the menu if I load a save, its just that the new character does not get the menu for some reason.

Well for me MCM doesn't work correctly unless i install the http://newvegas.nexusmods.com/mods/42507 after PN. I do see the option without it, but it does nothing.