Upgraded from the beta client to release 2 and now find that my old folders on my d: drive can no longer be added, only folders under my c:/docs and settings/user. I have a separate drive for data and this is where my documents resides.
I think you are talking about Ubuntu One on Windows.
You could try to create a Juction (a NTFS symbolic link) inside your User folder, that point to folder in D:. Here you can download the Junction utility: http://technet.microsoft.com/en-us/sysinternals/bb896768
I have not tried it, but may work.