With the EJB-based scheduler service, timer persistence is the responsibility of the EJB container. jBPM will save Timer objects to the database, but it is up to the EJB timer service to execute them.
Check your EJB timer configuration. In JBoss AS the persistence policy implementation in use handles if and how timers are persisted. By default timers are persisted to an in-memory database, saved when JBoss stops. It may not be able to save in the event of a system crash.
For details on EJB timer configuration refer to the administration and development guide.