SD Directoy/Files Disappearing

On 11.04 AMD64, directory and files on SD cards (I have two 32GB cards, one Kingston and one generic, behaving exactly the same way) consistently disappear. I have copied and pasted directly to the card through a card reader and to the card while loaded in a music player (a Rockboxed Sansa Fuze) to the same result. I have successfully reformatted and tested the file system on the cards numerous times and transfered bulk directories and files into directories individually. I have absolutely no problem with copy and paste/drag and drop (both behave the same way). Once they are transfered, I can see and play the music files without any problems. All Ubuntu music software sees and plays every song in every directory. Once the cards or the music player is ejected from the computer and re-mounted (the cards directly or from the player), the file system shows the same amount of used space but I cannot see most of the files (top two directory structures are visible for every band in alphabetical order ie. Card Name: / Music / Band Name) from the player or from Ubuntu. I can see the directory structures and the files fine in the first 11 or 12 directories (Structure being: Card Name: / Music / Band Name / Album Name / Song.*) but all other files and directories below Band Name disappear. I have the same result eliminating the top directory on the SD card of "Music". I know they are there since the exact amount of space is seen as used from "Properties" before and after unmount and mount. Any ideas what may be happening? By the way, CTL-H in any directory shows me nothing that I can't see before its execution. Thank you!