Thought the latest update might fix the problem but it still, popups notification every time I start mac. Have to go to the preference panel to select "None" in Notification to turn it off. Any help? Thanks!
What is the actual notification you are seeing? Is it saying something about it being downloaded from the internet? If so, that has nothing to do with Notification Center; that's just a normal alert.
In any case, this is a bug in OS X. You can either reinstall Hazel for just your account instead of machine-wide or you can fix it via the command line. If you are comfortable using the command line, the reply back and I'll post the command you need to use (or search the forums as I believe I've posted it here before).
I have rules running, for example, moving files from desktop to Downloads folder. When file was moved, notification popups from top right corner. Have to go to preference panel to disable notification every time.
That's different if it's happening for every file event. If you want to turn off Hazel notifications altogether, you can do that in your Notification preferences. If you just want to turn off certain types of notifications, in Hazel, you can select the Notification Options in the gear/cog pulldown.