Is there a way to ensure that the wyupdate.exe will not run right after the new wyDay.Controls.AutomaticUpdater() but only when i call the .ForceCheckForUpdate(true)?
Yes, set the "UpdateType" property to "DoNothing". Then, before you've checked for updates set the "UpdateType" property to "Automatic"
I am afraid I have witnessed times that the wyupdate.exe has run by itselft and the updates have downloaded and installed and not triggered by my code.
That's by design. By default the AutomaticUpdater automatically updates.
Then if I run another instance of my application (on another folder), the updates aren't working, it seems like more than one instance of wyupdate.exe is not working.
The AutomaticUpdater should work with multiple instances of apps -- I just tested it and it works here. What do you mean by "not working"? I assume all the instances of your app are running from the same EXE, correct? That is, you don't have separate folders for each instance.