Maybe I haven't explained myself correctly - I haven't created the animal companion as a separate creature, i've created a druid and added an animal companion to that character in Hero Lab.
When I level up my druid and then click on the companion, it's only letting me add +1 to ANY stat (not +1 to str and dex as per the PHB) and is trying to give it a feat and skill points.
I'll post some screen shots to explain what I mean
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