The Adventurer's Armory version of the Scorpion Whip currently does not work with whip proficiency, despite it being stated within Adventurer's Armory that "If you are proficient with whips, you can use a scorpion whip." Note: this is different from the Ultimate Equipment/Ultimate Combat versions which are also listed as weapon choices.
Now this has been reported in the past and the usual response appears to be that the rules surrounding the scorpion whip are too vague. However, the rules for the adventure's armory version are clear "If you are proficient with whips, you can use a scorpion whip." If you need further proof I've linked a reddit post with multiple instances of developer decisions on the matter.
Overall, if you are proficient with whip, you should be proficient with Adventurer's Armory's Scorpion whip as well.
PCGen v6.06.01, Java 1.8.0_31-b13, Windows 10
Should look something like this
Hmmmm, I put it in exactly like that (making sure I added a TAB before hand) and after saving and firing up PCGen again I still seem to be taking the non-proficiency penalty.
Is your whip user taking the feat Exotic Weapon Proficiency or is it
granted whip elsewhere?
He's getting it from the Bard weapon proficiencies.
Bah, okay, modify it to this:
BONUS:WEAPON|TOHIT|4|PREMULT:2,[PREMULT:1,[PREABILITY:1,CATEGORY=FEAT,Exotic Weapon Proficiency(Whip)],[PREWEAPONPROF:1,Whip]],[!PREABILITY:1,CATEGORY=FEAT,Exotic Weapon Proficiency(Scorpion Whip)]