Hi coach - Hmmmm...not sure. Restoring a library program should overwrite everything except the Global Settings. Unless, you saved your modified factory programs and it is now using those versions as the default version (see bolded text below). If you changed your Setup settings to include Discrimination in Common, that might also cause it.
I would walk through the steps below and make sure that you are selecting the library factory program(s) to restore...and double-check the Discrimination > VDI Select By > VDI > Edit values. Don't forget to restore Common as well. I have reset my v back to "factory settings" by simply going down the list and selecting/restoring each program to factory/library values. I had to do this when creating the spreadsheet several times when verifying values.
I have a feeling I'm missing something here, but it's propbably something simple.
Note: If you try to Store a factory program in the library there is no Save button, so it is impossible to overwrite the factory programs in the library.
From the manual (page 29)...
Spectra keeps copies of all the original factory programs in its Library. The modified and Saved program
automatically becomes the default version immediately available from Live Controls and both Menus under PROGRAMS.
There are ten Programs kept within the standard PROGRAM listings (Live Controls, Menu, and Expert
Menu). However, many more PROGRAMS can be kept in the Library. Keep the most used PROGRAMS under
standard PROGRAMS, and store the less often used PROGRAMS in the Library.