Yeah sorry about that - unlucky. Here's how I do it - you're free to ignore me ....
- do everything from a liveCD; saves issues with the pseudo f/s like /dev and /proc
- pre partition and format the new disk
- "cp -a
<source partition> <target partition>"
(repeat as necessary - not swap)
- mkswap for new swap(s)
- install the bootloader for new system
- fix the fstab (in need)
All done. The reason I use "cp" is that it is file-system aware, so you can be sure the files were o.k. (at least readable), and you can change the f/s format without issue.