Well the problem wasn't with the custom gametypes that were *already* on the server before this problem began, they were with the new ones that I added. After I wiped the server though, I had to re-add them all, and now none of them work because of that. In other words, all the gametypes below (S-Snipers, TS-Snipers, CTF-Snipers, etc.) were working just fine but when I went to add a new one called "S-Regs -s" it wouldn't recognize it in game as an existing gametype. So I tried a bunch of things and eventually reset the server and uploading all of the gametypes again, and none of them work now.
My init file looked like this:
sv_name "! Snipers by Havok"
sv_mapcycle_add bloodgulch "S-Snipers"
sv_mapcycle_add ratrace "TS-Snipers"
sv_mapcycle_add damnation "CTF-Snipers"
sv_mapcycle_add carousel "TS-Snipers"
sv_mapcycle_add hangemhigh "CTF-Snipers"
sv_mapcycle_add chillout "TS-Snipers"
Those custom gametypes like "S-Snipers" and what not are no longer recognized even though they are in the FTP in the proper location (account/halo/cg/savegames/gametype).