In every mission package Lunar or Planet Bases and Orbital when you have to do an "auxiliary module" mission the requested mission to unlock has wrong name, for example it searches Kerbin Orbital Station - Command Module but the mission is named Kerbin Orbital - Command Module, in Bases Packages to, it searches Kerbin Surface base - Command Module but the mission is named Kerbin Surface - Command Module, same thing for every auxiliary mission, so i've corrected all 4 .mpkg, now it works
simply replace this 4 files in GameData\MissionController\Plugins\PluginData\MissionController
https://mega.co.nz/#!8I4TxLzA!4Heb3I6-YRlgFNHCcHgS3UFYnhDXHCtYI3B7Y64v9EM
or
[dead link removed]
All "Auxiliary Module" missions will be unlocked correctly