The build dialogue box settings in MP mode are a mess and have been since FPSC beta, though that was not accepted by TGC. Use the defaults and edit the result in the final game build folder if you want to change the settings and replace the any default media with your own. You can change some settings in the editor dialogue box successfully but the whole lot of settings in that box are unstabe and behave erratically in MP game mode so its best left well alone.
As to the "Waiting to Join" message - I dont believe that happens for any one definative reason but more likely its behaviour and appearance is about as erratic under differing circumstances and amongst various users as is the behaviour of the dialogue box and is partly due to the erratic and unstable behaviour of the MP environment and during MP level complie.
Personally I tracked down long ago my own waiting to join error down to having teleporters in my MP levels and thats an absolute certainty - I tested it out long and hard enough to prove this to be the case. It has nothing in my case to do with ports or firewalls or any of the other suggested solutions. Changing any such settings never, ever made any difference to me - my firewall is a far more accurate and professionally well designed piece of software than is FPSC - without any issues - which is not the case with FPSC (MP environment at least) which is where the fault lies.
Simply - my MP games using exactly the same game levels and settings (or different ones) with a teleporter in them return a permanent waiting to join error - remove the teleporter and recompile and the game works fine - try it as many times as I like the result is the same. No teleporter = no problem.
Others get the waiting to join message and dont have teleporters in their levels (could be another no - no entity or setting used) so it certainly can be caused for more than one reason and that is not defined to specific perfection.
If you cant isolate your problem in a particular case then you would be best to forget MP until the update and see if anythings been done to improve any of it.