Hi littleshopoftreasures,
In order to post an item in more than one eBay category when listing through Auctiva, you should just need to select the first category from the "Category #" section of the Auctiva lister page and then select the second category from the section just below that labeled "Second Category".
I'm not aware of any technical problems that would cause the first category to become automatically deselected upon choosing a second category so that sounds like something we may need to look into further.
If you continue to experience that problem, I recommend contacting our customer support team about this using the form on the following page of our site:
http://www.auctiva.com/help/requesthelp.aspx#-Mike