when trying to build an Operative and work out what was happening, and looking first at troubleshooting.html then at LST files, I found that the bonus from Skill Focus (3) is stacking with Insight bonuses when it should not.

In troubleshooting, I see that

• when you add a Rank to a Class Skill, we see a variable "skill name" value 3

• when add Skill Focus, without ranks, the same variable appears as 3

• with ranks, class, and skill focus the bonus shows as 6
  so clearly the skill is being hacked directly.
  in scr_skills.lst I find

###Block: Skill Focus Support
Acrobatics.MOD BONUS:SKILL|Acrobatics|3|TYPE=Insight|PREABILITY:1,CATEGORY=FEAT,Skill Focus (Acrobatics)
Athletics.MOD BONUS:SKILL|Athletics|3|TYPE=Insight|PREABILITY:1,CATEGORY=FEAT,Skill Focus (Athletics)

so yes, the code is adding 3 directly to the skill.
Curiously Skill Synergy is coded very differently.

Profession (Archaeologist) KEY:Skill Synergy ~ Profession (Archaeologist) CATEGORY:Internal TYPE:Skill Synergy BONUS:SKILL|Display ~ Profession (Archaeologist)|2|TYPE=Insight|PREVARGTEQ:CS_ProfessionArchaeologist,2 BONUS:VAR|CS_ProfessionArchaeologist|1|TYPE=SkillSynergy CSKILL:Profession (Archaeologist)

this actually applies a BONUS:VAR to CS_Skillname