Adam, are you sure all the files are mp3 or another format that the Clip+ supports? If they are protected WMA(the default format that Windows Media player Rips to), then I suggest that you rerip them to mp3 files.
While the player can play protected WMA files, it has much shorter battery life playing protected files, and the player must be in MTP mode when the protected files are transferred, and Windows Media Player(or another Media player that also transfers the licenses) must be used to transfer the files otherwise they won’t play.
If you don’t need to use protected files, I suggest the usb mode of the player be set to MSC, and that MP3 files be used, a even with unprotected WMA files, battery life is much worse than with mp3 files. If the files are all mp3 files, and the usb mode of your player wasn’t set on MSC, and you have copies of all the music on your pc, I suggest formatting the player using the player menu(settings, system settings, format) which deletes all the songs off the player, setting the usb mode to MSC(settings, system settings, usb mode, MSC), then connecting the player and copying the music to it.
Are you sure your tags are in order? The tag browsing on the Clip+ is not true tag browsing, but a recreation from the database table, which depends on the tags. are your mp3 tags ID3V2.3 ISO8859-1 which the player expects? Do those files that the player skips over play okay on your pc?
What are the other stats for the mp3 files that don’t play? Are they at a non standard sampling rate or bitrate?
Are they constant bitrate or variable bitrate?
If you are using a memory card, make sure it is class 4 or slower. The Sandisk players have many issues with faster cards, except that when the free alternative firmware(operating system) Rockbox is used, class 10 cards work fine.
If you don’t have any protected files, you could try the free alternative firmware(operating system for the player) Rockbox, which has many great features, and much greater flexibility in terms of the files it supports(except that it doesn’t support protected files). I have Rockbox on my Sandisk Clip+ and Clip zip. Rockbox.org