Upon rereading the release notes, I do see that there's a bugfix for this in the 5.4 beta builds:
"Addressed an issue where the Stencil Window search could recognize certain files that are not stencils based on their file extension."
So, go try out the beta build at
http://www.omnigroup.com/products/om...oad/sneakypeek and see if it works better for you.