I've done a little more research on this. It appears that the edit window appears with the same dimensions of the User Note Window at the time the edit session is initiated. So, if you only have a couple of windows open (vertically aligned) there is sufficient window width to display the auto link button. However, if you have several windows open and vertically aligned (Say... two translations, two commentaries and then your user notes window) then the window size is narrow and when the edit session is initiated, the edit window is also narrow and must be expanded.
A modification to allow more control over the default size of the edit window would be great. Either a "remember" previous session size or a default edit window size. For me, increasing the font size is not a viable option and I'm not sure that would even work since the "current" window size seems to be trigger for the "edit" window size.