It gets tricky tryIng to get everything to sync. I had to have ms1 in its own main neo geo folder and it had to sync first. Then I had to have ms2 in its own neo geo folder and it had to sync last "6th". 64 doesn't work great so it's not worth it so I took it off. I have 677 nes. 19 snes 10 genesis 5 gba and 2 neo.
Would be really curious if you could have both metal slug's in 1 folder on the new version.. The whole syncing 1 folder for 1 game, which represents "neo geo1" is silly to me as well. I don't like that and if that's how it works with me then I'll be removing it.
If I follow the instructions that were posted above, I believe I just add the modules, THEN add the games and make the new Neo Geo folder.
One difference between our setups is you have GBA, and I've read bad things in regards to using it on here. I would be curious if you removed your GBA what you would get.