I have this problem with Win Defender,
When i reboot my computer, Win Def gives this warning in a popup ballon from the system tray.
"An application registration change was made to C:\program files\windows defender\mpcmd run.exe"
When i click on the balloon it just disappears,but Win Def does not open as is normally the case with other warnings.
What does this mean?

open WD and read the info and then decide to allow or deny the change. Clicking the X in the balloon only closes the balloon.

tried that but when Win def opens there is nothing there. The "history" section is also empty.
I'm sure that when other warnings have come up,clicking on the balloon opens Win Def to allow/disallow the changes.

You are correct. WD sent updates to me this AM and I only clicked on the balloon and the update window opened. If you are still getting this alert, probably the easiest fix would be to reinstall. Back several months ago when I installed WD it said it was free until July. I haven't heard if that is still true. I have decided to switch to Spyware Doctor rather than pay for WD.

Is Spyware Doctor better?

It would take a lot of testing by someone much more skilled than myself to determine that. It is my understanding from reading info on both that they pretty much do the same thing as far as monitoring goes. The free version will monitor and keep malware off your comp the same way WD does but while it will identify malware during a scan it want remove what is already on your computer.