Ok, delete any icon for BD Rebuilder from your desktop, delete all files pertaining to it (outside the helper programs AviSynth, Haali, and ffdshow).
Use the direct download from Videohelp.com: http://www.videohelp.com/tools/BD-Rebuilder
Make a new folder called BD Rebuilder. Put the zip file you downloaded from Videohelp.com into the BD Rebuilder folder. Unzip it here. You'll now see another BD Rebuilder folder within the new one you just made. Open it and you should see all the files and folders. Right click on the BD Rebuilder executable file and run as Administrator.
The paths to the tools are done internally, so you can't adjust them. All you can do is unzip the package, but maybe getting it from another source and doing it this way will eliminate the error.
Also run the Inspect.exe program and see if the helper programs are set up properly.