I am running iTunes 12.3.2.35 on OS X 10.11.3 beta 1 and so far I am unable to replicate your problem. What specific screen are you trying to configure? Are you looking at Songs, Albums, Artists, Composers, or Genres? Only in the Songs screen are the columns adjustable and only in that view can you configure which columns are visible and FWIW I can adjust all the columns and select which columns are to be displayed without difficulty.

I looked at the iTunes preference file and as far as I can tell the information on which columns are visible and the column widths would appear to be stored elsewhere — I know not where that may be confused You might try creating a new iTunes Library (hold down the option key when you launch iTunes and see if that clears the issue.

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