Okay, so did some more testing. Bought a new Samsung Evo + 32GB card and prepared it on my laptop this time.
Did a full format with SD formatter, put the beta pack on there and overwritten the menu with the one DS posted.
Still MV-1F mobo with unibios 3.1
First boot, straight through to the menu (this used to take me 3 tries minimum), I was able to see ALL games, even including Windjammers, which I've never seen before, hooray!
The shortcuts to go back to the menu and switch slots still don't work though. I either get filesystem not ready, no games found or when it does go to the menu I only see like 20 titles or something.
It also doesn't keep any games in the buffer, not with a softboot, not with a reboot of the cab (PSU).
Also, an interesting fact is this timeline:
1: go back to menu by using the shortcut, filesystem not ready no games found
2: reboot by using unibios reset method: error with the green overlay screen
3: reboot cab by switching off/on the PSU: no games found
4: reboot cab again - tadaaaa my games are back in the 3 slots
5: play Magician Lord (slot 1)
6: go back to menu by using the shortcut, slot 1 and 2 are empty, only slot 3 shows a game
7: game 3 autoboots (Sengoku 3) goes straight into green overlay screen on title screen
Go figure? I'm lost here
So I've ruled out the SD card I think as well as the SD reader/writer since I've used 2 physical machines and multiple ways of formatting.
What else can I check for?