James Jacobs wrote:
In the 3.0 rules, bonuses to natural armor from amulets, barkskin, and other magical sources did not stack with a creature's natural armor. As a result, amulets of natural armor rarely appeared in adventures as part of a monster's gear.
To address this fact, in the 3.5 rules, the bonus granted from an amulet of natural armor, barkskin, and similar sources is now treated as an enhancement bonus to existing natural armor. Thus, a monster with a natural armor bonus could wear and benefit from an amulet of natural armor.
This can certainly impact the difficulty of an encounter, but no more so than having a monster with high natural armor wear a suit of armor or wield a shield. In many cases, monsters can't wield shields, and even wearing armor is unusual (or just plain silly; an iron golem can wear a suit of plate mail and gain a +8 AC bonus, but it looks goofy); for these monsters, the amulet of natural armor is now a viable option.
Thanks for the help guys, I think I was remembering back to my 3.0 days, lol. I realize now that the two should stack!