Okay if I were you I would not worry about using Mamescan. I have never gotten Mamescan to work for some reason. You don't need Mamescan to get Game Launcher to find your games. In your Mame.cfg, just set it to scan for games automatically instead of using the mame.rom file. This way, whenever you start Game Launcher, it will automatically scan for all games and create the list based off that scan. And as for the remapping of the names, just goto your Mame folder in DOS, and type this command:
mame -listfull > mame.map
It will create a file called mame.map. Place that file in your glaunch\config folder. That's it. You are all set to go.
Also regarding your NeoGeo problem, make sure you have the Neo Geo bios rom files. That might be a problem if you don't have those. But anyways, I'd go with my solution.
jakobud