Windows may not allow copying of the system files.
You can follow DOC's (Richard Cranium) suggestion to connect the problematic drive as a slave drive. Boot into DOS mode, use
md c:\olddata
c:\windows\command\xcopy32 d:\. c:\olddata\. /s/v
In the above commands, I assume that
- your backup drive is bootable and you can boot to DOS mode.
- your backup drive is the master drive (C

- the old and problematic drive is the slave drive (D

.
This should copy all the files (including system files) from your old drive to the backup drive.
-Screen