Since this is a problem i purpously made mine into a pk3, with instructions on how to install it.
For those server owners who simply shove the modded qvm in base/vm, don't.
Here's instructions on how to change the mod name:
1. create a folder in ur appdata/trem folder. Name it to [the real mod's name such as [W]onderland or BenMachine etc...]
2. Create another folder within that folder called 'vm'.
3. Shove the qvms in it.
4. When running ur server, before you start it up, don't forget to set 'fs_game' to [what the real mod's name from step 1].
When a client connects, he probably won't download a thing if the mod is simply just qvms, autogen etc., but his computer will create a new folder called [whatever you named the mod's folder], and creates a new autogen.cfg etc. blah blah blah.
That should make the modded servers have different game names.