Windows 7 Professional SP1 64-bit
Similar to these bugs:
I lose some highlighting intermittently throughout the documents during the Compare operation. After I click "Clear Results", I lose all highlighting.
I think that http://sourceforge.net/p/notepad-plus/bugs/4091/ is a duplicate of this problem. Does this plugin need some updating after recent changes to NP++?
I got version 18.104.22.168 at https://sourceforge.net/projects/npp-compare/?source=dlp and this problem seems fixed for me.