Here's a run through, can't contact WooThemes(Commerce) directly. :(
WooCommerce Wont Save Colors (VIDEO)2 posts from 2 voices
I believe that is because the theme overwrites those styles and so it locks the changing of them. So if you wanted to change a color of an item that would normally be done with those options, you could either change one of the main styles via the theme options or if you can point us to the exact items you want to change we can help you with CSS to target them specifically.
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