Metal Slug 3 and Real Bout FF Special by any chance not working?
I am 99% sure the BIOS are giving you issues.
@Okko and I have found the fix/solution.
1. Take your neogeo.zip BIOS and extract the files into a folder, then remove the neogeo.zip from the folder.... Now remove these files if they are present...
uni-bios_3_3.rom
uni-bios_3_2.rom
uni-bios_3_1.rom
2. Search for and download the free and legal current uni-bios 4.0 BIOS. Now extract to your desktop and rename the file to (uni-bios_3_0.rom).
3. Now drag and drop the file you just renamed into the extracted BIOS folder. Yes overwrite the file when prompted.
4. Now highlight all files inside the extracted BIOS folder and ZIP the contents naming to (neogeo.zip)
5. Now drop the NEW neogeo.zip into the folder where your NEO roms are, start WFL and for example sakes, select and boot Metal Slug. Most likely you will get the famous NEO bios boot.
6. Press Home on Wiimote...scroll to and select Options...scroll down to and select BIOS...scroll dow to and select Universe BIOS ver. 3.0.
7. Now Quit RetroArch, back to WFL and boot Metal Slug again. Neo-Geo Universe BIOS 4.0 should boot now...
If you press A,1,2 simultaneously during BIOS screen you can change between USA, Europe, Japan Arcade or Console BIOS. Some games have extra content available in Arcade mode, other things are altered depending what region you set also.
Hope this helps you out and these new modified BiOS work 100% with both RA and SS-Hexaeco.