I believe this is actually a Hero Lab bug.
When SoM grants ranks in a sphere's associated skill, it does so by adding to that skill's skExtRanks field, the same way a Fighter's Versatile Training ability does. I tested just now with a vanilla Fighter, and Skill Focus is not granting the full bonus to characters with ranks gained through Versatile Training either. A quick look at the code for Skill Focus will show that this is because it doesn't count the value of the skExtRanks field when deciding whether to increase the bonus.
I can think of one or two ways I could work around this, but I would prefer to either let Lone Wolf fix the feat behavior, or find confirmation that this is actually intended and rules-compliant before I change anything. If anyone knows of a confirmed Paizo ruling on this matter, I'd appreciate a link.
*EDIT* - Asked on the Paizo boards:
https://paizo.com/threads/rzs42yal?Virtual-skill-ranks-Skill-Focus#1
But awaiting an answer.
Digging a little on the Paizo boards...
A lot of these seem to be answered by non-Paizo people, but no one is then correcting them.
Not sure if that counts a rules ruling or not.
Most of the search is either the word Versatile or Training, not much that are actually the two words together.
The only mention I saw of Skill Focus was the bard's performance which was via virtual ranks but not directly asking if virtual ranks get the higher bonus at 10+ virtual ranks in the skill.
From the wording, I think it would since you're counting as having the ranks and it's not a bonus. As per the first question, except the response was from a player, not from a Paizo Staff.
https://paizo.com/threads/rzs2taom?Fighters-Versatile-Training#1
Question on whether the Fighter gains the +3 bonus for trained skill with Versatile Training.
Answer: The fighter is gaining actual ranks, rather than a +X bonus to a skill, so they should act like skill points in the skill and get the +3 bonus.
Not a Paizo answer, but no one contradicted the poster.
https://paizo.com/threads/rzs2jueg?Versatile-Performance#1
Asking if bard's virtual ranks in two skills by virtue of having the Performance that is used in the place of two skills, do they need skill focus in the skill or in the versatile performance skill.
Answer: The rules say they use their total bonus from Versatile Performance (which would include skill focus in that) in place of their relevant skill it's replacing.
That doesn't mention +3 or +6 bonus at 10th.