Sounds like you’re transferring DRM-protected WMA files over in MSC mode which is likely to be the issue. Make sure your Clip is connected in MTP mode and try again using the different programs you mention to Sync those files to the Clip. Any DRM-protected files with licenses will not transfer the license if you use MSC, so you must use MTP for getting these files to the Clip.
Remember that you’ll only be able to see the “songs” in Windows Explorer that were transferred in the current mode of connection, MSC or MTP. Thus, if you use DRM files a lot I would recommend making sure all the songs are transferred over in MTP. You’ll have to delete the songs (or move them to your computer if not backed up so you can get them back to the Clip later) that show up while connected in MSC mode, disconnect & wait for rebuild database to complete, reconnect Clip in MTP mode, and then re-transfer over those deleted (or moved) files in MTP mode. Hope this helps!!