If you create work planes, solids, dimensions or other components in an RFA file, then rename the file extension to .RFT for use as a template, the original items you create cannot be deleted. We're working around this by creating a startup families folder underneath our family templates, so the user can simply open this file, and then use Save as to create their new family.
Chris Aquino at Autodesk helped me out on this one - they put a post on their blog as well:
The day you know everything is the day you retire...or when your kids have children of their own - that's when they figure out you were right all along...
later - David B.