Sounds like it to me.
In my past experience, you load missions/maps into correct folder, then start the game up. As long as you have the same version of the mission as the server you are connecting to, there should be no problem.
Pretty sure you cannot have the game running, tab out of it, load another mission version into custom levels, then tab back into the game and select it to play.......you have to come out of the game completely for this to work.
Also, I have come across in the past that certain maps can interfere with eachother if left in the custom levels folder and prevent you from playing the latest one you installed.
Get into a habit of having the latest maps in the custom levels folder only and installing new maps even before you start the game up. If you do this, you shouldnt have any problems.
cjo1964