Sorry for the delay in response. But we are closed on the Weekends, and therefor, Monday is a busy day for support.
The options are ordered by the order you entered the options, so if you added the size options and then the color options, then the order will change.
If you send me a link to your product detail page and tell me what you expect to happen i should be able to assist you. Most likely we will just need to change the ordering to order alphabetically.