Have you tried adjusting the play count parameters?
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Having all three of those checked doesn't make much sense. You either want the cover embedded in the file, you want it saved as folder.jpg, or you want it saved as something with a custom name. I doubt you want all three.Agreed.
Since you list Cover.jpg as your first choice for display, it probably makes the most sense to uncheck the first two.I will try that and see what happens.
Your files need to be tagged properly (correct title, artist and album name) for artwork to be found by the tools in musicbee. It is very rare that I've been unable to find artwork through MB's tools, and in those instances it's usually things like old or off-label compilations.I believe they are tagged properly. The vast majority are ripped from commercially available CDs.