PROBLEM RESOLVED:
Having run out of ideas to try, I ended up backing up my SNES build to my PC and used that SD card to put the SGB2 on. That worked perfectly. The card that didn't work was a Sony SR-8C4. (micro SD) I wonder if it has something to do with the controller on the card? I tried it several times and with that card it never worked, so it seems if you are having problems just try another SD card.
The SD I use is one that pops out of the device by pushing it down and always sticks out a bit, it's a much older model though even have ones dating back to the very 1st Krikzz Super Everdrive too. Glad to see you managed to resolve the issue, I'm hoping in the future their will be a way to interchange the boarders between non SGB enhanced games like how the EDGB managed to, likely a menu reset may do the trick but it's so jarring when you get used to it just to find out you had to power off everytime to play a new rom for Gameboys series and the fact it always starts at the SNES devices menu screen is hard to get used to as well though the correct clock speed is nice however as my device is PAL it's hard to tell the difference unless you come from NTSC territory xD
As for cards from memory it goes in this order...
Original 1st version Super Everdive = Blue 32GB Sandisc SD card (No card inserted into the reader as it's a big blue one) [Fits into device hard to ply out)
Common 2nd version Super Everdrive = Same Blue Sandisc spare SD card (Once again no card inserted into the reader as its a big one aswell) [Same issue as before wasn't until the SD2SNES when ejecting a card was made easy with a spring]
Default SD2SNES = Grey and Red Sandisc 64GB Micro SD HC A1 card with reader included (Device can eject card with spring easily)
Clone SD2SNES = Kingston 16GB Micro SD HC with reader (Pretty much the same as the default official SD2SNES with the exception it cannot run MSU1 but does on all other chips)
