You might try cutting a "patch" out of an old tube, putting a hole in it, and slipping it over the valve stem. This would provide protection around the stem, should prevent a burr from puncturing. BTW-I also have stems with the threaded thumbnuts. The only time they are against the rim is when I'm inflating the tube. After tube is inflated, I back them off to about halfway up the stem, so they can't bind or pull at the tube.