Q: Attempting to delete duplicates, "show exact duplicates" checks all instances of some songs

If checking one entry in a list checks another that makes me suspect that you are looking at a playlist into which the same items have been added more than once, rather than the main Music listing. The checkboxes are global throughout iTunes. One of the phases in my deduper script mentioned below will clear such playlist duplicates, however in its current form you would need to run it on each playlist where you have this problem if you only want to fix that type of issue. For cleaning the library start with the Music source in the songs view and use exact duplicates. The current version requires disc counts and tracks counts to match which I'm not sure has always been needed. If you're not seeing all the duplicates that you would expect that might be why.

Apple's official advice on duplicates is here: Find and remove duplicate items in your iTunes library. It is a manual process and the article fails to explain some of the potential pitfalls such as lost ratings and playlist membership, or that sometimes the same file can be represented by multiple entries in the library and that deleting one and recycling the file will break any others.

Use Shift > View > Show Exact Duplicate Items to display duplicates as this is normally a more useful selection. You need to manually select all but one of each group to remove. Sorting the list by Date Added may make it easier to select the appropriate tracks, however this works best when performed immediately after the dupes have been created.  If you have multiple entries in iTunes connected to the same file on the hard drive then don't send to the recycle bin.

Use my DeDuper script (Windows only) if you're not sure, don't want to do it by hand, or want to preserve ratings, play counts and playlist membership. See this thread for background, this post for detailed instructions, and please take note of the warning to backup your library before deduping.

(If you don't see the menu bar press ALT to show it temporarily or CTRL+B to keep it displayed.)

The most recent version of the script can tidy dead links as long as there is at least one live duplicate to merge stats and playlist membership to, and should cope sensibly when the same file has been added via multiple paths.

tt2

Show duplicates doesn't check or uncheck songs. It also doesn't make any suggestion over which of say 4 duplicates of the same song you should keep, and which you should throw away. However my script does exactly that for you. There are two main phases to the script, the first analyzes the library and prepares for the deletions in the second phase should you proceed to make them. In doing do it actively checks the track that will be kept, copies the highest rating to it, adds the play and skip counts from the other copies and then sets them to zero, sets the most recent play and skip date, and makes sure this track is added to all of the playlists that the other tracks are members of. The potential discards are all unchecked. If you have alternate duplicates (different sized versions of same songs) it will also preserve the oldest date added value by swapping the pointers between two files if needed. I added this last feature so I could preserve the date added information for the tracks I recently upgraded from 128k DRM AAC to 256k DRM free AAC with iTunes Match. If you cancel the second phase you can review the proposed keeps and discards before they are actually enacted.

If you need me to expand on this step-by-step guide for running the script please feel free to ask.

tt2