UPDATE: The T reports the pass problem has been fixed in time for the evening rush.
There were two dead trains on the Red Line this morning. Meanwhile, Kristin MacDougall tweets she asked a woman at a customer-service window at Downtown Crossing what to do about the fact that her July pass didn't work:
Woman at T Cust Svc window said: Bad batch of July passes indeed went out. Should work in 2 days. Till then, duck or piggyback.