I've had a look at the registry file that Shawn provided, and this might be the cause of the problem. Some of the entries pertain to the HKLM branch, and these can only be modified from within an administrative account. At the same time, the other entries (the HKCU ones) will be restored to the values in the file, but only for the administrative account. Other accounts will not be restored, and they will use the values that they had previously.
I'm going to split the file, and you should merge the first one (the one pertaining to HKLM) from an administrative account and the second one (HKCU branch) from each account separately.
Files superceded. See my next post.