you did something wrong, you must replace C and copy E folder contents to the xbox HDD (read the instructions, you must have a full copy of the 5960 MS dash in a folder called "C" in the installer dir and then point the installer to it when it asks)
start over and delete all the files in C:\ first using FTP, then FTP the NDURE installer for PC "C" files to the xbox HDD then copy "E" the files
So by starting over you mean;
1. Hotswap and restore the backed up \C\ contents from the backup I have.
2. Download the 5960.01 dash from somewhere into a working ndure directory on my pc. (how do I know if this exists on the backup I have?)
-from the ndure 3.0 readme.pdf-
3. Patching C drive files:
For this, it is recommended that you have latest MS dash (5960.01 V. 185EAD00). Have all of the dash files in a folder named "C". Next, run the installer with your appropriate choices. As a destination folder, select the parent folder that has your dash files "C" folder in it (don't select "C" folder). The installer will add/rename/delete necessary files and create a complete C drive replacement.
3. Run the ndure installer using this working folder as the target. (what does the above mean by "all of the dash files")
4. Using ftp delete all of the files from the \C and \E directories on the hotswapped drive.
5. Copy the ndure target directory over to the hotswapped drive.
6. Reinstall the HD and Reboot?