'Show scroll bars' stuck on Always
I fixed this by editing the AppleShowScrollBars string in the ByHost .GlobalPreferences plist.

Even though ~/Library/Preferences/.GlobalPreferences.plist showed the correct value of ‘WhenScrolling’, the ~/Library/Preferences/ByHost/.GlobalPreferences.udid.plist had the value of "Always". By changing the string using Xcode and logging out, it was resolved.