I have the same problem, after viewing files on my laptop through the USB port.
It took me half the night to fix, I had to copy all the files to a folder on my laptop's hard drive, remove the phone, delete all stuff on the card (through the phone, there was no option to "format"), then paste everything back to where it was.
I noticed that there is no option to "remove safely" before unplugging the USB. I looked everywhere, even installed their program, but there's no eject or the like. Apparently it corrupts something.
If you google this is a major problem (disappearing media) but the Android developers, Phone manufacturers, and Carriers just point their finger at the other guy, nobody fixes it.