Multiple issues with iTunes/iPhone Music Library

I have been having several problems with the new update (for the iPhone and iTunes.)
First, when I download music from iTunes, I always clean up the album names (for instance, if I download an album that is called "Can't Stop Me - EP", I always remove the "EP" part, etc. That includes anytime it says Deluxe or Single. I have always done this to keep my library clean, but since the new update, every time I fix it, I'll close iTunes, and when I reopen it later, some of the media I change reverts back to the original name. If I check info on the media, the name I changed it to is still there, and when I click "OK", it reverts back to the new name. Why is this? It is also never consistent, and it picks random media to revert every time I go into iTunes.
Also, one other issue I am having is I am seeing duplicates of artists in my Music on my iPhone. Avicii shows up twice with the same media listed under his name. What's weird, is that when listed alphabetically, the letter "E" appears above one of the duplicates. If I try to erase it, my phone crashes and both Avicii's disappear. If I sync my phone, the duplicates reappear and the cycle repeats. It does this for a few other artists in my library as well.
I've tried resetting my phone and it fixes the solution for a bit, but then it happens again. Some solutions would be appreciated. Thank you.

I had not tried that before, but from your suggestion, I went ahead and did it and it seems to have gotten rid of the crossfade issues I was experiencing but whenever I try and listen to a preview in the iTunes music store it still does not appear to be working.  Also, I was testing a number of tracks and it seems like there are a few tracks in particular that will make iTunes stop playing when I click on them and then if I attempt to play something else, iTunes says it is playing but no sound is coming from it. 
What I have found that is interesting is the first time I ran the Disk Utility it repaired a HUGE number of misc. files.  After running it and still experiencing problems I tried to run it again but this time the files were not as numerous and were all within the /Library/CoreServices menu.  Each subsequent time I ran the Disk Utility and rebooted, I tried to run the Disk Utility again and the same files seem to still be having the same issues.  This is just an example of one of the files I have been having an issue with.
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/zh_TW.lproj/RemoteDesktopMenu.nib" , should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/zh_TW.lproj/RemoteDesktopMenu.nib" .
One in particular gave me a Warning and said it could not be repaired.  I'm not sure if it is important to repair but I still seem to be having some issues here and there.  Here is the message from the Disk Utility regarding the file in question.
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.

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    I had not tried that before, but from your suggestion, I went ahead and did it and it seems to have gotten rid of the crossfade issues I was experiencing but whenever I try and listen to a preview in the iTunes music store it still does not appear to be working.  Also, I was testing a number of tracks and it seems like there are a few tracks in particular that will make iTunes stop playing when I click on them and then if I attempt to play something else, iTunes says it is playing but no sound is coming from it. 
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    Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/zh_TW.lproj/RemoteDesktopMenu.nib" .
    One in particular gave me a Warning and said it could not be repaired.  I'm not sure if it is important to repair but I still seem to be having some issues here and there.  Here is the message from the Disk Utility regarding the file in question.
    Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.

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    http://i51.tinypic.com/2prxxet.jpg

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