Ah, the Simply, I remember when I abused it.
There are a few things:
1) I'm not sure, but I think Rune Factory 2 had some copy protection or a bug along those lines, but I'll need confirmation.
2) You could try the old 'backup and reformat' with your MicroSD card.
3) This could also be the result of a very common problem that happens with some flash cards and other 3rd party cards. The pins could be very dirty, so I recommend opening the shell (it should use a small phillips head) and doing the following:
-Dip a Q-tip in some rubbing alcohol.
-Give the pins a good scrub. It's likely that they will leave a dark residue on the Q-tip.
-Use the dry end/another Q-Tip to dry it off
-Leave it in a small room on a hand towel with a fan on to cycle dust and whatnot off.
-Reassemble and try again.
Number 3 is a guaranteed method, as anyone on the M3 forums will attest to. It also works if your card decides to not launch all the time.