This sounds a lot like the problem I am experiencing.
Thing is the images I have downloaded or taken with my X are not deleted, they just do not show in the Gallery or other media viewers, but the files are still on the SD card itself if you use File viewer to locate them.
If that is the case i've been informed that there may be a folder called NoMedia created on the SD card which is causing the problem. I know I have the folder since I created it not long after getting the X to store images I did not want to show in the Gallery (guess it works overtime!) so by deleting that folder you should be good. I can't get access to the file system from work so have yet to try it but shall do so when I return home.
Actually, would a system reboot/restore lose all my files or just return the Phone to it's default look?