The Clip is capable of connecting to the host PC in one of two modes, MSC (it acts as a basic flash drive), and MTP (communicates protected media files with Windows Media Player). The problem between these two modes is that, on the PC, files transferred in one mode are not visible while connected in the other mode.
The hiding of files was a Microsoft invention, intended to “simplify” things for you, separating modes.
The sansa will find and display the music files regardless of mode used for the transfer.
To switch modes, with the sansa disconnected, go to settings > USB Mode. Just remember, for secure WMA file transfers, you’ll need MTP.