Elemental weapon damage in Diablo 3 doesn’t receive a benefit from the “+X% Damage” item affix. It’s broken, and only affects “black” or non-elemental damage. If a weapon has any elemental damage, it doesn't properly calculate the +X% damage to the weapon. It’s broken, and it’s been broken since the game was released two years ago.
In other words, if your weapon does 1000-2000 Fire Damage and contains a +10% Damage affix, you won’t be doing an extra 100-200 points of damage even though you should be.
Blizzard has since acknowledged the issue, and today, we finally have word that they are going to be doing something about it in the game’s upcoming patch.
Posting on the battle.net forums, QA person Tsarnis wrote the following post to inform users about the development and what their plans are with dealing with it:
I just wanted to pop in here and let you know that we have a potential fix in place for this internally and it is currently looking like this fix will retroactively apply to existing weapons. While we will not be able to deploy this as a hotfix, we currently expect this fix to make it to live servers with our next game patch. I obviously can't make promises as to when that patch will arrive, but it is something we are actively working on, and we hope to be able to get that deployed as soon as possible.
Thanks again for all of your reports. I know it took me a bit of time to get back to you, but your patience is greatly appreciated!
We'll be sure to keep you updated on the development.