Scratch the last post, I redid some nagging question areas from tests I did a few hours ago (last night) and I think I now have it locked down.
It is "not" just the alternative Stat issues that were causing the issue. But it still only impacts on Throwing items only.
It appears what is happening, is that somewhere during the code, it is taking the original attack modifier used for the base item, and THEN subtracting your new stat modifier for attack from that initial amount. The greater the difference between the two numbers, the greater the number you will notice (which is why it's much more noticeable at cap when your primary stat is so much further ahead of the base stat that is used).
eg.
Shuriken (Dex base), with Falconry it becomes (Dex, Wisdom)
With 25 Dex and Wis modifier, there will be no difference.
With 25 Dex modifier and Wis 38 modifier, it will become 25 - 38, becoming "minus 13" modifier after it is applied to this thrown attack.
So in
@Larendell case we can see in their stats that they have an Int modifier of 36, and a Dex modifier of 8, so if we apply the same we get 8 - 36, giving us "minus 28", which when we apply to their difference is roughly the same.
Will be conducting more tests on this a bit later on to confirm more on each part that needs more clarification (like what happens when there are three or "more" attack modifier stats, etc). But the jist of it is there.
J1NG
:: edit ::
OK, so tests with Brutal Throw correctly utilise Strength as the main attack bonus and doesn't have an issue even though a Shuriken used which is normal Dex based had a difference or 3. So the Feat effect appears to be OK here.
With regards to having more than 1 bonus to attack stat on a weapon (Dex, Int, Cha for example) the system only uses your highest stat and the base stat and subtracts them as the bug works right now (as described in this post). So those with more than one stat for attack need not worry other than if your stat is clearly far and above the base attack stat of the Thrown Weapon.