Are you placing a file in cfg/maps/<mapname no .bsp>.ini
You would need an ini file for every map you had that you wanted to use that gamemode.
So, say you have a gamemode named I_Know_Jack
You have two maps. IKJ_1.bsp and IKJ_2.bsp
In your server cfg folder, you'd create a folder named maps
in gmod/cfg/maps, you'd create two text files, one named IKJ_1.ini and one named IKJ_2.ini
Inside each file you'd put sv_gamemode "I_Know_Jack"