Problem: I relied heavily on NTFS Junction points in Windows XP, even though they apparently were not an \"official\" feature of the operating system. Now MSFT
Why don't you try with this program (freeware) to create the links. Apparently Windows Vista needs a different version. I have tried both versions (XP and Vista) and they work. I know it doesn't have to do with your specific problem, but given that there are separate versions for each OS, there might be diferences in the way Junctions are created.
The tool you have used is rather old (2007) and doesn't mention Windows Vista. I know that MSFT did change something in the Junction Points in order to add some functionality they wanted to use. Vista is more authoritative when it comes to Program Files folders and such.