Welcome!
First, are all the albums DRM-free, and in a format recognized by the Clip?
Second, avoid the Auto USB setting, by all means–the computer can do things without your knowing (switch from USB MTP mode to MSC mode). Likewise, USB MTP mode can do things which surprise–I would stay away from it as well, unless you need it to play DRM-protected files.
In the end, I’d delete the user content on the player to get a fresh start, set the player to USB MSC mode, and then transfer to the player anew–hopefully, that will fis matters! 
