Partition clone not copying all files
I am a new user to Backupper so am not terribly familiar with it. I have a computer with 2 disk drives and several partitions on each drive. I'm installing a new drive with enough space to copy all of the partitions from the original 2 drives to the new one. All of the partitions have copied in full except for the system partition where Windows is loaded. Here is a report of what the differences are after doing a partition clone (not sector by sector):
I'm assuming that I'm not following the proper procedure to clone the system drive but I'm not finding anything in the forums or FAQ that gives me any clues as to what I'm not doing correctly.
Any help would be appreciated!