I'm back from a long vacation from gaming. I upgraded and loaded up my characters. Then went about cleaning up all my custom code that has native HL code. Here is my first list of problems I've identified.
#1 Issue Int items not granting ranks in chosen skill
Book: CORE
Items that grant an enhancement bonus to Int used to grant skill ranks in a skill chosen. The code exists to select the skill, but the ranks are not being granted. I can't be certain, but I believe this once worked and currently does not.
Example: Buy a Headband of Vast Intelligence +6, pick three skills, and notice they are still at 0 ranks.
Fixed previously.
#2 Issue Inconsistent policy on Int bonus granting skills items
Book: CORE and Seeker of Secrets
The Crimson Sphere has a Simple object that detects how many, but doesn't put a line item (like Headband of +6 Item does) for the user to select a skill to add ranks. The Scarlet and Blue Sphere does ask for a skill. My interpretation is there should be skill ranks assigned for both and there should be a way to instruct HL to do so.
Example: Buy 2 Crimson Sphere Ioun Stones and 2 Scarlet and Blue Spheres. Notice no skill ranks or skills are chosen for the Crimson Sphere.
Got this fixed I think, there is a delay in whether the 3rd selector shows for the skill if you are combining cracked and normal versions, but it will show once you perform some other action (like add or subtract a skill point).
#3 Issue Second Darkness PrC Chevalier allowed with second darkness source disabled.
Book: Second Darkness
Second Darkness prestige class Chevalier isn't tagged against Second Darkness, and I can't locate it in any other book. It should be unavailable if you do not have Second Darkness checked.
Example: Create new hero, uncheck, second darkness, add Chevalier levels.
Added the Second Darkness source.
#4 Issue Plumed Mantle provides In-Play Flying but other Flying items do not.
Book: Core
Some items that allow the user to fly are able to be activated, but some can not be.
Example: Create new hero, buy Winged Boots, Broom of Flying, Carpet of Flying *, Cloak of the Bat, or Wings of Flying and notice no Flying check box in In-Play. Then buy Plumed Mantle and notice it has a check box.
Here's my thoughts on this. Broom/Carpet don't grant flying to the character, they are ridden instead, so they shouldn't show a fly speed on the Specials tab at all.
Winged Boots, Cloak of the Bat and Plumed Mantle all grant flying as the spell (with some competence bonus) but with a limited duration, so they need an activation.
Wings of flying are worn on your back and grant you a continuous fly speed of unlimited duration (and don't mention it being as the fly spell), so they show a fly speed on the specials tab when equipped.
#5 Issue Horseshoes do not add their abilities and can be worn by non Quadrepeds.
Book: Core
Horseshoes of Great Burden and Horseshoes of Speed don't grant their abilities.
Example: Create new hero, buy a horse, give it horseshoes, equip.
I'm uncertain whether enforcing the the "Must be Horse-shaped to wear horseshoes" thing is worthwhile. It's not as simple as just requiring a quadruped, for example a lion is a quadruped but shouldn't be able to equip horseshoes. This means I'd have to go back through the back monster catalogue and mark each one with a new "Horseshoes OK" tag. I'll check into it, but no promises, k?
Both the example items you noted have eval scripts for their effects as of the UE update.
#6 Issue Improved Natural Attack can't be taken for Natural Weapons when the weapon isn't currently on your Hero
Book: Bestiary
A Hero with Wild Shape should be able to take INA of a weapon that is available when in a Wild Shape, the feat will go red (as it should) when not currently Wild Shaped into a form with that weapon and go normal when in a form with that weapon.
Yes, there should be a note saying this may not be allowed by your GM. But as it is now if you give yourself a weapon and make a selection, when that weapon goes away after the Wild Shape is removed you lose the selection made.
Regardless of the GM decision, the selection needs to be retained beyond saves.
I've got a custom one that modifies "Restrict First List to... All Things"
Example: Create druid, activate a template granting a slam attack, make a selection on INA feat, deactivate the template taking away the slam attack, save and reload the portfolio, activate the template, and notice your selection has been removed.
Oh Druids! Why must your wild shaping ways always break my heart?
That said, I am not sure that druids of a race that doesn't already have a natural attack qualify for Improved Natural attack, since one of the pre-reqs of the feat is a natural attack. And even if they do have one from their race, I am not sure they could pick a different one, an attack that exists only while they are wild shaped.
I'm going to leave this up to DMs to houserule and modify the feat as necessary (as it sounds like you have). As for the selection resetting when you remove a weapon that was there, I don't think there is anything I can do about that. Perhaps you could have your version of the feat bootstrap the particular weapon you are interested in (you could even give it a Hide.Weapon tag so it didn't show on the Weapons Tab), and rather than using the default selections, enter your own Candidate expression that doesn't exclude hidden weapons. Then you could always pick it, because there would always be a copy present, but it wouldn't muck up things on the weapons tab by being present when it shouldn't.