I've modded a couple of systems before, and I've noticed on some when I connect via FTP (FlashXP) I sometimes see a 2 extra folders, folders H and folder I, though I never bothered to opened them up..

Has anyone seen this before? if so what are these folders for?

They are memory cards plugged into controllers.

You can use them as kinda portable storage by FTPing any files across to them you want. 8Mb isn't much but it could come in handy!