I have found that using the phone as a USB drive mounted seems to be the problem. I use a regular usb card reader and the micro adapter. I then transfer music and video to the card that way then reinsert it into the phone, reboot, then plug in the usb cable once and unplug to force the rescan of the card and I have lost no music in over a week now.
I format the card on the window system in FAT
Fat or fat 32 should be 32.
Beamed from my SteelDroid D3