Had a similar sitch in USSSA men's slow-pitch. The pitcher was intentionally covering the rubber, according to his "reasoning" it was better protection. Since USSSA has the pitching box, he reasoned we should be able to call the unfairly delivered ball without a problem (mind you, the lines had been wiped because this was the 3rd game of the night). I told him no, you need to uncover the plate, and the only time I will not have an issue with dirt covering the plate is if it happens during the course of play. He refused, so I called his first pitch unfairly delivered, and next thing I knew, I was sending his sorry a** to the parking lot. Sheesh.