I never noticed that the Compare plugin caused Notepad++ to be unstable. But there are some other plugins doing so, e.g. MenuSearch and LocationNavigate. Especially MenuSearch is weird because wether it causes problems depends on the presence and/or absence of other plugins. At my site it works fine if NppFTP is installed as well.
You should try to install one plugin after another and perform tests after every installation until you find a plugin which causes problems. Then uninstall all other plugins and test the suspicious one alone. If it works fine start adding other plugins until you are facing problems again. Then remove all plugins except the first and the second suspicious one and repeat the sequence.
This way you will find combinations of plugins which effect each other in ways that make Notepad++ become unstable.