Folders are resorted in the restore view and do not appear in the same order as in the backup view. If you have a very long directory structure, it might appear that certain folders in that directory were not backed up, however upon closer examination, you should find the subdirectories listed lower down the directory tree.
The main reason why this would seem like the files were not backed up is also due to the fact that the directory might have contained files in a very distinct alphabetical order, like the use of names, for example:
Then, you have a name or folder like: ckelly
And this is where the confusion happens. In the restore window, the restore view is sorted alphabetically to a point, but case-sensitivity takes precedence here. In the Restore view, folders are sorted alphabetically/numerically first, then upper-case, then lowercase. So, if you have a folder that is like such, they would appear like this in the Backup vs. Restore views:
So quite simply, the backup view, much like the directory view on the OS respects Alphabetical order/Numerical Order while the restore view respects case.