What glitch? Can you provide more information?
Game saves created on system software 6.x and up, will always appear as corrupt on a system downgraded to 4.x
If you set up a 4.x emuNAND and boot it with rxTools, it will still show as corrupt.
After placing the slot0x25KeyX.bin at the root of your SD card, and updating your emuNAND to the latest version, your games created on ver. 6+ should play fine without "corruption" messages.
If this doesn't answer you're going to have provide me with more information about this supposed "glitch".
-snip-
Edit: Perhaps I was being more of an asshole than I intended to be. Full post quoted below as a permanent reminder for me not to be a dick.
I am trying to boot Alpha Sapphire and my emunand is on 9.5.0-23U, with KeyX being green on the rx menu, my sys is on 4.5. When it boots it still shows as corrupt, then i put Alpha Sapphire into my brothers 3DS which is on 22U and it doesn't show up as corrupt.