When selecting Skinwalker Heritage, Ability Score modifiers should adjust to reflect the ability scores gained from that heritage. For instance:
Expected Behavior: a Wereboar gains +2 Str, -2 Cha, and +2 Con when shapeshifted. (Normal Skinwalkers gain +2 Wis, -2 Int, and +2 [choice phys stat] when shapeshifted.)
A similar issue is that for some reason PCGen seems to be accounting for MULTIPLE modifiers to the non-physical stats. For instance, before selecting a Skinwalker heritage my ability scores were displaying -4 Int, +4 Wisdom (instead of the +2/-2 expected.)
Once Wereboar heritage was selected, it is now showing +4 Wis, -2 Int, and -2 Cha. There are two problems with this, one is that it's accounting for two separate sources of modifiers. The second issue is that the source of both modifiers is wrong. (There should be a bonus to Str in there somewhere, and a negative to Cha. Instead there is no bonus to Str at all, and there is a random penalty to Int which doesn't belong. Additionally, two bonuses to Wisdom are there which don't belong.)
One of the problems is obvious. Even after a heritage is selected, it is still applying the base Skinwalker racial to the ability scores, which it should not as heritages modify the base. The second issue is not so obvious, but it seems likely that the data for the WereBOAR heritage is not correctly input. (Ie, currently is incorrectly listed as +2 Wis -2 Int whereas expected/correct behavior would be +2 Str -2 Cha.)
It appears the heritage ability scores are both not properly identified, and are not properly overriding the base Skinwalker racial ability scores, when a specific heritage is selected.
Fortunately it is allowing me to upload this save file, so you should be able to see what I'm talking about.
Paizo Publishing: Blood of the Moon, Win 7
Congratz! We finally have an issue I can fix!
Unzip and replace the existing with that. Let me know if that fixes your issues.
Also, I need an errata or citation from the publisher that the Wereboar has those stats - my copy of the book is "Ability Modifiers +2 Wis, -2 Cha (+2 Con while shapechanged)"