You may just have too many addon missions (the game does have an upper limit). I would first suggest moving some of your addon maps or mods to a different folder (you do not have to delete them, but they will need to be moved temporarily).
There is no reason that any map or mod, unless it is a true side mod, would affect conquest and nothing else (especially 1flag or CTF, because those use the exact same units). I would bet that you hit a mission limit - am I right in assuming that you have at least one other "big" mod installed (Dark Times, BFX, Mandalorian Wars, Prime Front, etc.)?
Just for yours and anyone else's edification, the upper limit is 500 addon missions (not maps). Every game mode added by anything is a mission. The Conversion Pack is the "heaviest" mod in the game as it adds about 345 missions. Dark Times, by comparison, adds only about 35 missions. Any "big" mod is going to be a drain on this mission limit as will any addon map (although a single addon map usually only has between 1 and 5 missions). I would not recommend having more than about three big mods installed at once (although remember that they do not need to all be installed at once to use them; you can simply move their addon map folders in and out of your addon folder whenever you wish to use them).
ill try that, though i only have convo pack installed.