Changing spec order makes optimal stat distributions disappear?

Character specific
1

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As you can see from the above snapshot, my Hunter has an optimal all green stat distribution when Beastmastery is in the second position after Survival.

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Change Beastmastery to priority one, and bam, I lose 0.03% DPS and, more importantly, with the same items in my bags, I suddenly have no gear that gives an optimal stat distribution!

I understand that the order matters; it matters in determining what kind of gems or enchantments I apply if I have only one high iLvl piece of armor for certain slots and so on, but if I have multiple pieces of armor for almost each slot, and I have a gear set that gives an optimal stat distribution for a certain spec, why would the order matter in this case, especially in this strange way?

Is this a bug? If not, then what is the reason I don’t have an optimal Beastmastery stat distribution when it is priority one?

2

I’m not sure why it want’s to change the neck item… something to do with the gem/enchant threshold. It probably shouldn’t change the neck item. If you lower the threshold on gem/enchant to 0.25%, it seems to do a better job.