I beleive it has to do with the marks they leave on synthetic lanes. My father, before he had a stroke, threw nothing but LT-48's. When the centers in our area went to synthetics they told him he couldn't throw it anymore. He was forced to move into Urethane. I am guessing this center probably went through the same thing and just decided to ban rubber balls altogether.
The problem I would see with that, obviously, is that if the ball is USBC approved, regardless of coverstock, how would the house be able to dictate what a bowler can or cannot use during a sanctioned league?
Yes, I realize the house is the house and theoretically they can do "anything they want", but one issue I could see being raised is that if the house wants USBC certification, they have to abide by USBC rules, and USBC rules say I can use any and all approved equipment, including rubber balls. I could see somebody, somewhere, making a stink about it to the local association, and the center getting into hot water with USBC because they're arbitrarily banning approved equipment simply because their lane men or mechanics don't want to do their job.