I made a thread about this issue in November, but I wasn't able to get this issue resolved. http://forums.bistudio.com/showthread.php?185160-Missions-that-used-to-work-on-dedicated-server-no-longer-work-on-dedicated-server
That thread has links to the Whatthefuckdidyoujustsay.Takistan pbo and the mods it uses, which may be useful for troubleshooting.
One very strange thing I noticed when looking through the rpt files is that it said that I couldn't play doomsday_night_3 because it is depedent on wapaddon when I know for a fact that the mission doesn't use that mod. This is in the arma3server_2014-12-19_06-02-10 log.