Hi thegolfshop,
When the store window is added to your listings that were not originally created through Auctiva, it is added as an appendage and, therefore, appears at the bottom of each listing below the "On 29th May seller added..." statement. However, since the store window is set to appear at the top of your listings in the "Edit Store Window" section of your Auctiva account, for any listings posted through Auctiva, the store window will appear above your description.
The only way to remove the store window from your currenty listings to which it has been appended would be to edit each listing using eBay's "Revise your Item" form and moving the store window HTML from the bottom of your description HTML to the top. Of course, this could only be done in listings that have not received any bids and have greater than 12 hours left. If you are interested in giving this a shot, you can catch a glimpse at what your store window HTML looks like by clicking the "Store Window HTML" link under the "Store" tab within your Auctiva account.
-Mike
