I would rename the directory to upper-case, but it is our file server and is hit rather hard at times so I can't change the directory name (open files and what not).
As an experiment, you could try copying one of the problematic file trees to another location and see if rsync still fails to access it. Though I'd try the other offered suggestions first.
(This doesn't explain why none of the files in those directories were transferred, but keep in mind that if you're backing up an in use server, rsync won't be able to access any files that are locked for reading if the files are hosted on a Windows server. You can avoid this by hosting these files on a Linux/Samba server.)
Where /cygdrive/e/ is the drive I'm backing up, and /cygdrive/z/ is a Samba mounted shared on the Windows server...
FYI, you lose the benefit of rsync if one leg of the transaction is a network mounted drive (SMB, NFS, whatever). If performance is a concern, run an rsync server on the machine supplying the Z drive.