OK, you have the correct keys and they should be programmable but I suspect that you are going to have to take them to the dealer.
You seem to have a different version of the manual from me but this excerpt would appear to be relevant :
Activations through diagnosis instrument
The DUCATI diagnosis instrument allows performing a series of activations to check some instrument panel functions and resetting parameters or warning lights.
After each activation, the instrument panel will restore its standard functions.
Note
The activations must be performed only with key turned to ON, engine off and battery voltage ≥ 11.0 V.
Immobilizer (keys) reset
This activation allows "erasing" the "keys" to reprogramme the Immobilizer System.
Upon receiving this request, the instrument panel resets the previously stored keys.
Upon next Key-On, the Immobilizer System will be "virgin" and it will be possible to reprogramme new keys.
Programming the Immobilizer System
When replacing the instrument panel with a new one or when reprogramming the Immobilizer System
(because one or both keys got lost).
If the System is "virgin", upon Key-On the instrument panel immediately activates the "Immobilizer
Programming" mode.
Programming procedure:
- insert KEY 1 (one of the two black keys) and turn the key from Off to On;
- within 3 seconds turn the key from On to Off;
- within 15 seconds insert KEY 2 (the other black key) and turn the key from Off to On;
- within 3 seconds turn the key from On to Off;
- within 15 seconds insert KEY X again (no matter if Key 1 or Key 2) and turn the key from Off to On.
- If the procedure was successful the instrument panel shows "PROG." and "OK" for 3 seconds and then
switches to the standard display mode.
Although this procedure appears to be for resetting the immobiliser it involves erasing and re-learning the keys. It also requires the Ducati Diagnostic instrument to initiate the procedure.
The key duplication requires the erasing and re-programming of the old keys as well as the new keys :
The Ducati authorised service centre will program all new and old keys.
So it is almost certain that the Ducati Diagnostic instrument is required.