The first was one they warned about, how Cygwin stores mount points. These are no longer stored in the Windows registry, but are instead read from /etc/fstab. Cygwin comes with a script who's purpose appears to be to create this file for you, but when I ran it nothing happened. So I was left creating my own /etc/fstab. Here's what mine looks like:
C:/cygwin/bin /bin ntfs binary,user 0 0
C:/cygwin/etc /etc ntfs binary,user 0 0
C:/cygwin/home /home ntfs binary,user 0 0
C:/cygwin/var /var ntfs binary,user 0 0
C: /c ntfs binary,user 0 0
C:/Documents\040and\040Settings/don/Application\040Data /n ntfs binary,user 0 0
C:/Documents\040and\040Settings/don/My\040Documents /m ntfs binary,user 0 0
W: /w ntfs binary,user 0 0
Y: /y webdrive binary,user 0
The second issue I ran into was that I didn't have /bin or /usr/bin in my PATH. The previous versions of bash/cygwin did this for me. I actually had a line in my .profile commented out that would have done this. I simply put it back in and was good to go.
So far these are the only issues I've had with the upgrade and they were relatively easy to fix.
