i too have exactly the same issue, let me explain..
i was using my phone (xperia arc), browsing some files in gallery
then there was a random reboot, i thought it was an issue with the ROM,
all my apps were deleted(i was using sd-ext partition),
all the settings were altered (screen lock removed, all incoming call were blocked, and a lot of other things)
i thought it was some kind of VIRUS,
then in the end i discovered that my SD-CARD is showing exact behaviour as mentioned in the first post
i dont know what to do with it, tried almost everything, any help would be great!!