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Sendric, that code was mine. It was there so that races would automatically calculate and increase their saves as they gain extra HD.
What I would do is add that +2 back in, but also have a check before running any of the automatic calculation scripts on the types. If the race has more than 0 racial HD (I can't think of a humanoid with racial HD, but I am sure there must be some), then run the script to calculate the BAB/saves/skill/etc, otherwise don't because they will be defined by class levels (for humans and the like).
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