Supplied character had multiple core sources loaded:
This resulted in multiple copies of the companion mod bonuses being applied.
Issue discussed in email chain:
The issue seems to be derived from the Black Blade familiar.
What seems to be occurring is when it assigns the bonus stats to give it the correct Int/Wis/Cha it is giving it a +2 instead of the +1 for a level 3 character.
Originally i thought it was related to installing a 5.0 dataset but after wiping the installation and doing a fresh install the issue persisted.
Attached is the character in question so you can see what sources and so on are being loaded.
While most other types are filtered to ensure only a single copy is loaded, the ABILITYCATEGORY and COMPANIONMOD files may be loaded multiple times. This was demonstrated by loading Pathfinder RPG Core Supplements, Pathfinder RPG for Game Masters, and Pathfinder RPG for Players together while listing the LST files loaded. Only these two types were duplicated.
These files now use the same duplicate filtering strategy as other file types.