There are 2 ways of getting music from Amazon (and also Rhapsody). You can purchase MP3 music directly, or you can subscribe to their service(s) that provide slightly higher quality music files in a DRM crippled form.
To make use of the later (DRM’ed) files you would need to “sync” both the music and licenses with the player (which requires connecting in MTP mode). And, you also have to periodically update the licenses on the player in order to continue playing those specific music files. It sounds like you’ve done this at some point even if you may not have intended to.
MP3 files do not have any form of copy protection, so it you have MP3 files they should still continue to play (even if the other DRM’ed ones do not).
I’m not sure if/how this may have any effect on the player working when plugged into the Timex clock though.
If you really don’t want to ever mess with DRM’ed music and/or subscriptions services, the best way to clean things up would then be to re-format the player and start over with putting only non-DRM crippled music files onto it. Even then, you may still run into problems when connecting to your computer for certain things and may also need to use whatever software that initated things to de-authorize the player so that everything forgets about it.
