I had this problem pop up recently each time I tried to start Notepad++, my editor of choice. I uninstalled the version I had and installed the latest version, which was 3.9 at the time, which seemed to fix the problem.
Until today, when it would once again just give me the stupid “System Err” popup, and not start. It seems reinstalling over the existing installation doesn’t fix this, you have to uninstall it first and then reinstall to make it work. Which might get pretty annoying, if you have to do this every couple of days.
All Google seems to know about this is in French, but it seems those guys too have just the uninstall/reinstall solution for this. They do seem to recommend even deleting any remaining files after uninstalling and before reinstalling – specifically
nppshellext.dll which for some reason doesn’t get uninstalled propery.