Unfortunately, the only mk3 format options are within menu 0.6. You can format the mk3 and neo, but not the menu flash??
Do you have a 'mk2_save' file on your sd card, created by menu 0.4? If so, you can try deleting that...
I assume you reformatted and maybe defragged your sd card, so basically, you just have clean dumps on the card, and not .sav files from previous menus....
With menu v.4, did it not ask you to save/load or did roms just not run??
However, now it gets stuck in .6 beta 2, when asking to load/save/or erase mk2, so that's why you can't even boot roms??
BruceG