Hi pdxmatthew,
Thanks for your suggestions, because all the notes share a common parent window you get that behavior unfortunately but it's something I'll look into. You can actually change all the settings in the Preference dialog, and it will store them all, but it should really have an Apply button I guess like a traditional wizard. Your 3rd point is also valid, but you can resize the note after you minimize it and it does try to size it to size which displays either the first line of text in the note or the title you've set for the note.
Regards,
Karl