We found the issue, it was happening when the user had moved away from their main window. For example, opened up Chrome, added an appointment (which open a 2nd window), they added their note, but then used the 2nd window to go back to their dashboard and accounts. Because they had 2 windows open they then where closing the first. The second time they add an appointment it was from this 2nd window which opened up a 3rd. For some reason Chrome then does not allow the pop ups. I think it is because it is a window of a window.