I apologize for not returning to this thread much sooner.
Eventually, I found out what happened, and it had nothing to do with id3 tags. Two things contributed to the problem:
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I deleted songs from the clip+ without emptying the “trash” bin and
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I removed the clip+ from the usb port without selecting the “remove safely” option first.
I can only assume that emptying the “trash” actually deletes the songs from the clip+ for good (at least in Ubuntu), and not doing that after removing the player probably makes it think that the songs are still there even though they are not, which is why the “refreshing media” screen does not complete.
Since I figured this out, I haven’t had any problems to speak of.
