Both cygwin and cmd.exe showed the junction points I created as valid, yet PHP's require_once couldn't read them.
I did notice some strange output in the DOS listing of the junction point which got me concerned:
11/16/2009 05:47 PM
After a bit of poking around, I learned something amazing - Windows 7 now comes with soft and hard links built in. The right command to use is mklink.
I replaced my old call of:
junction target existing-dir
mklink /J target existing-dir
And now the link was created correctly - PHP, cmd.exe and Cygwin were all happy.
I'm amazed. Finally, Windows gets file links. Look at that, baby's growing up.