If you took a full backup, its a VHD file of your old drive, which can be mounted as any other VHD, or restored, but since a VHD amounts to a full disk image, it restores a drive and partition, not really the data on the partition. If you look in the disk manager you can attach a VHD as any other disk image and it will show it as just another harddrive.
Wonder if you ran into some error if there was an old boot block or some other thing relating to the former partition that went away with the clean command. Or of it had something to do with the geometry of the new vs. the old drive. Especially since the Windows format nowdays uses padding to align the partition with the drive blocks.
This is what Microsoft page says about clean...
"Use the clean command to remove partition or volume formatting from the current in-focus disk by zeroing sectors. By default, only the MBR or GPT partitioning information and any hidden sector information on MBR disks is overwritten. If you specify the all parameter, each and every sector can be zeroed, and all data that is contained on the drive can be deleted."