Artemis Mod Loader simply dumps the mission into the folder per the instructions for adding missions, so the issue really shouldn't be with Artemis Mod Loader (i.e., it just does the basic file copy into the mission folder).
HOWEVER, the latest version (1.702) did break a lot of the missions built for the older version. Make sure you are using the latest version of the missions.
ALSO: "The Eagles Wrath", "Doomsday Revisited", and "Clouded" are ONLY valid with the "Star Trek: Into The Breach" Mod. These use ships not defined in the unmodded Artemis, and will thus crash unless you have the mod applied to all clients and server.
Finally, Hamak Sector is designed for the plain, unmodded Artemis. If you are using it for the Star Trek: Into the Breach Mod, that could be why you are having problems.
[Last edited Jul 10, 2013 17:19:12]