Hmm = think I have found the problem. When you load a mission in the editor and then save it under a different name a new directory is created in your user/.../missions directory to hold the new version of the mission. The pbo-packer then operates on this new version to produce the pbo that gets dropped into your MPMissions dir. It appears that only the mission.sqm file is copied across to the new version. If you keep the original name of the mission when you save it, all files are already present in the missions directory and get packed properly into the pbo.
BTW, if you were wondering why I was changing the name of the mission, it was because I am fiddling with a mission that requires respawn to test. That means running the mission in multiplayer mode and because OFP doesn't seem to release the file-lock on a mission file after you have finished playing it, I have to keep saving new versions to different names :-(