My character Minerva Nirax of the same login isn't getting the +2 bonus for 10 secondary intimidate. I did the whole rest, reload class perks, relog, transition, and wait for server reset to repeat it all. She only has what is given from charisma modifier and equipment. She does not have any cross-class skill points in the Intimidate skill though, which is largely why it is being taken as a secondary skill with primary being less available, so maybe that is a factor. Can't say I actually tried the old Secondary Diplomacy without skill ranks manually added also so not sure if it is doing like Jump where it won't add if you don't have base ranks already.