Well I did the same as sromeroi posted. I did it with Shock Troopers, used the bios_files.hmod template instead of using the core_template rename. Synced everything and was able to get the neogeo.zip bios into the correct bios folder, then installed the fbalpha2012_neogeo.hmod. Synced the game afterwards and it worked fine. I loaded it up and worked.
Thanks for chiming in.. Looks like the only difference is you didn't rename the core_template.. And maybe different Roms..