Missions don't run out of the offmiss folder(.mis files) anymore, they run out of the missres folder(.res files). Make sure you have the latest M.E. version. Open the missions up in the M.E. from your offmiss folder. When you open a mission up in the M.E., hit File->Build Res Library. That will convert your mission to a .res in your missres folder and should be ready to play now.