Has anybody used Shock Sox or any other neoprene fork protector on their conventional forks?  The boots on my bike are shot and looking at options.  The local old school suspension guy told me that any neoprene protector can trap and pump water into the fork tube.  Has anybody ever heard of this?

Shock Sox are designed to be used on upside down forks to keep rocks from scratching or nicking the chrome on the fork tubes.
Damaged fork tubes are what cause seals to leak.
Shock Sox are meant to be run loose, doing so on a conventional fork allows dirt and water to settle on top of your seals. This is bad.
Order up a set of stock rubber boots for your forks.
Don't be a poser, use the right part for the right job.