So there's this new problem that has crept into Magento 1.9.1. When you create a configurable product the attribute options resort themselves by the Simple product IDs instead of your stated sort order. To fix this problem you will need to apply the patch file that I've created below.
Step 1 : Creating the overriding file structure
You will need to create the following folder structure, because most likely it does not exist. This file structure will override the original file and allow you to maintain an upgrade safe patch to your Magento installation. I've bolded the local folder in this breadcrumb because it's where you will need to start creating folders.
Step 2 : Creating the patched file
Inside of the last folder that you created, Attribute, you will need to create a new file called Collection.php and paste into the contents of my patch below.