I’ve noticed that when I run SQL Validator over a project or single SQL statement while Application Designer is still running, I later experience issues in Application Designer. I usually experience a shared key or shared cache error. In some cases I find that I have to purge the cache (using Configuration Manager) before I’m able to successfully run Application Designer again. I’m pretty sure that the problems all relate to the fact that SQL Validator shares the same working cache as Application Designer.
Moral of the story: Close Application Designer before running SQL Validator.