I had the same issue and spent time looking for solutions.
In the end I decided the least risk “solution” was to sign up for itunes Match as I wanted some of my older MP3s uprated and wanted a streaming service where I owned the content after paying for it.
Backed up my music. Signed up for itunes Match, let it “match” everything then deleted my entire library. (NOTE IF YOU DO THIS FFS REMEMBER THE BACKUP FIRST).
Then I spent a good day or so downloading my entire library and basked in my smugness at no longer having duplicates…..
My smugness was however shortlived; many of the songs cut out after 30 secs….FFS! aaaargh! iTunes really is utter shit 🙂
Anyhow, after researching the issue I then deleted my entire library again. I disabled concurrrent downloads and forced it to download one track at a time.
I’m happy to report my library plays as it should now. £20-odd, many hours and barely a hair left……
The above sorted my library on my PC but on my iPads/iPhones I’ve gone back to syncing using iTunes as the downloads to the iPads also suffered the 30sec problem (unless you stream the album first).
Hope that helps OP – if you’re willing to punt another £20 at the problem – just remember to turn off auto renew….