The problem is most likely unaligned extended partition/volumes.
You should only move/restore an entire extended partition to a drive that has the same geometry as the original.
To fix this you'll need to do several steps, in general they are:
- Disable the Align on End option under Drive Settings (make sure the correct drive is selected).
- Slide the extended partition either direction so that it does move.
- Resize the end of the extended partition to be larger (say 20MB free inside).
- Slide all the volumes, starting at the end, down a small number of MB (say 8MB).
- Enable the Align on End option under Drive Settings.
- Resize all the volumes, keeping them the same size.
- Optionally, slide all the volumes back up.
- Optionally, resize the end of the extended partition to have 0MB free space inside.