After setting the sequence for product variants in Catalog Manager, the Commerce Server 2007 Starter Site still does not list product variants such as color or size in the desired order. They are always listed alphabetically.
To resolve the issue you will need to edit the control used to display product information.
Open the CommerceCommponents.csproj which is located in the directory where you unzipped the Starter Site. In the file 'pvcClient.js' find the line that contains the statement "values.sort();" (minus quotes) and comment out this line. You will now rebuild the Dll and then deploy to your site.
Now when you select the product variant drop down for a product, in the list displayed in the drop down the product variants will now be displayed as they were sequenced in Catalog Manager.