To reset bbNote location, just rename (i.e. delete-but-back-it-up) [font="'lucida sans unicode', 'lucida grande', sans-serif;"]bbnote.ini[/font]. A new one will be re-created.
I personnally copy-pasted the (almost) default settings to my [font="'lucida sans unicode', 'lucida grande', sans-serif;"]bbnote.ini[/font] (the lines with leading "!", which includes both the starting position and its size) :
...
[font="'lucida sans unicode', 'lucida grande', sans-serif;"]# by default :[/font]
[font="'lucida sans unicode', 'lucida grande', sans-serif;"]!wx0=108[/font]
[font="'lucida sans unicode', 'lucida grande', sans-serif;"]!wy0=303[/font]
[font="'lucida sans unicode', 'lucida grande', sans-serif;"]!wxl=688[/font]
[font="'lucida sans unicode', 'lucida grande', sans-serif;"]!wyl=643[/font]
[font="'lucida sans unicode', 'lucida grande', sans-serif;font-size:10px;"]# current settings :[/font]
[font="'lucida sans unicode', 'lucida grande', sans-serif;"]wx0=108[/font]
[font="'lucida sans unicode', 'lucida grande', sans-serif;"]wy0=303[/font]
[font="'lucida sans unicode', 'lucida grande', sans-serif;"]wxl=817[/font]
[font="'lucida sans unicode', 'lucida grande', sans-serif;"]wyl=732[/font]
...
So that I can overwrite the coordinates whenever I no longer see bbnote: close/kill bbnote, copy-paste and remove the "!", re-start bbnote.
Please note that may also happen with (at least) bbStyleMaker for which [font="'lucida sans unicode', 'lucida grande', sans-serif;"]bbstylemaker.rc[/font] is involved. That file only contains the last position of the window, e.g. :
[font="'lucida sans unicode', 'lucida grande', sans-serif;"]bbstylemaker.xpos: 836[/font]
[font="'lucida sans unicode', 'lucida grande', sans-serif;"]bbstylemaker.ypos: 206[/font]
Set both of them to 1 and it'll appear on your main screen (well, kill bbstylemaker, modify the .rc file, restart bbstylemaker).
Final information : that behaviour occurs when you use 2 screens and you placed bbnote on the second screen. If you reboot with only 1 screen, bbnote will still try to be located on the second screen.