As to files not showing up on your computer:
When your player is connected to your computer under USB MSC mode (set under the player’s settings/USB Mode), your computer only sees the files that had been transferred to the player when the player was connected under MSC mode. Likewise as to MTP mode. Regardless, all the files show up and are playable on your player, under whatever USB mode setting.
A good reason why some people prefer to set the USB Mode on their player to either MSC or MTP: on the Auto setting, the player tries to connect under MTP mode but then will fall back to MSC mode if the MTP connection does not work; the result being, you may have a mix of MSC and MTP mode transferred files on your player, making some of them not visible on your computer without switching to the other USB mode.
Because MSC mode is more universal (playing with a broader range of operating systems, including Linux and on Macs, and without a need for Windows Media Player on the computer), some people prefer MSC mode. However, note that DRM (digital rights management) files need MTP mode–they will not transfer sufficiently (the DRM license will not transfer) under MSC mode.
To “correct” files not appearing: set your Clip to the other USB mode, transfer the Clip’s files to your computer, set your Clip to the other USB mode (the mode you’re going to keep your Clip set to), and transfer the files back to your Clip from your computer.