There's an issue with weapon proficiency when using the "counts as" feature. For example, the Barbed Bolas from Complete Warrior (community set) is set to count as the Bolas. Both of these are exotic weapons. If you take Exotic Weapon Proficiency (Bolas), you gain proficiency with both weapons. The problem is that when you are creating a new magic, custom, or masterwork weapon, the Barbed Bolas is greyed out as if you aren't proficient with it. Once you've added the weapon, you are treated as being proficient, but as you can see in the screenshot, it doesn't work until you've added it. Oddly, this behavior does not exist if you try to add the weapon under "Other Weapons".