After you’ve made your configurable product with more than one option, changing the order is simple.
1. Navigate to Catalog > Manage Products >
2. Select your configurable product record.
3. Associated Products tab.
4. Scroll down to Super Product Attributes Configuration.
5. Use the little orange arrows to move the attributes higher or lower.
Not so much fun to do this if you have more than 10 products.
However, if you have access to the database directly, for example, through phpMyAdmin, you can use SQL to do this really quickly.
The table where the order of attributes for your configurable product is located is named catalog_product_super_attribute.
The SQL code that fixed my little problem is this:
UPDATE `catalog_product_super_attribute` SET `position`=1 WHERE `attribute_id`=149;
UPDATE `catalog_product_super_attribute` SET `position`=0 WHERE `attribute_id`=148;
If this helps you, I’d love to hear about it.