Microsith has also screwed up mine. Backed up the data disk on the old PC, powered on the new one, restored the backup. Most of the file permissions are b0rked. Whole directory trees are inaccessible. Format drive, mount backup as a disk, copy everything over. This will take at least three hours. Bah.
I've only just noticed this thread, so too late to help, but a bit of info...
On A Windows system with an NTFS filesystem, all the files have an Owner, and also various Permissions for other Users.
This is called the Access Control List, or ACL.
In the situation where you have an existing hard drive containing files from an old windows install, and mount it as a secondary drive in a new windows installation, and then wish to copy files from the old drive to the new, then you will encounter permissions problems.
Because the User on the New System is not the same as the User on the old system, you are regarded as a wrong 'un, and access is denied.
Even if the User Name is the same, that's not good enough.
The User Name is just a 'Pretty' display name.
The actual 'user account' is a long unique ID called an SID.
The SID for user Fred on the new system is not the same as the SID for user Fred on the old one.
In this situation, you need to use your Admin account Fred on the new system to 'take ownership' of the files on the old disk.