I have the same problem. If I start it in Normal, Official, Team Deathmatch Mode (to get players in from quick match) then switch it to Conquest, it limits to 44 players. I did a chat with EA help and was told that it would switch from 44 to 64 once it was "stable". I'm not sure what "stable" means.
On the other hand if I start my server in Ranked mode, I can easily switch it from 20 tdm to 64 conquest. Of course, I have to invite 64 player friends to fill it up -- which can be very difficult to do when Battlelog isn't working (sorry, that's a different post).
