I had the same problem that the restoring data does nothing. The first attempt to restore the boot camp was successful and then I wanted to create the 3rd partition so I can dedicate that partition for my user data. After making the 3rd partition, my boot camp can't boot.
So I remake the boot camp partition using Boot Camp Assistance (skip the installation) and remake my 3rd partition and run Windows intaller to reformat the bootcamp so it can boot again. After all set restoring the boot camp partition using Winclone from image that I already moved to external drive. (The first one that successful was created from the image stored on the OSx partition and I have to move it to external drive because not enough space after creating the third partition) The restoring process from external drive (exFat) did not successful.
So I try to remake the image and store it the third partition which is an Mac OS Extended Journaled. That also doesnt work.
Here are my attempts:
Did not work (restoring from):
1. External Drive - ExFat
2. Internal Drive 3rd partition - NTFS
3. Internal Drive 3rd partition - Mac OS Extended Journaled
4. Internal Drive the main partition with total 3 partitions
Surely Works Image from:
5. Internal Drive the main partition (Mac OS Extended Journaled) with total only 2 partition (osx & boot camp)
My conclusion is you can only have 2 partition in order to works. I'm not sure if you can restore from external drive so far. Hope this will help anyone who want to experiment with upgrading hard drive with 3 partition. Sadly after 2 days attempt that's not possible.
MBP 2012 2.3hz, MT Lion, Seagate Momentus XT 750gb, WinClone 3.4 (3455)
FYI - the Momentus hybrid drive works great on OSX (half speed of boot and opening apps) but not that great on Windows or Parallels desktop (maybe only 10 - 30% faster)