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.
#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.
#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.
#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.
#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.
#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.