cannot clear error messages on our alarm pad after changing the battery,?

Our alarm was set off by strong winds and branches hitting the window. When I arrived home I suspected this had happened, but to make sure I tried to open the door which was locked. By doing this I set off another zone. After that, the battery light was flashing on the panel as well as the two zones that were triggered. Still unable to clear the panel screen and reset the security, my husband replaced the two batteries which both have power backup. That cleared the battery message light. The trouble light is still on, as well as the zone that I set off and other zone, which reads in the manual as Tamper-siren and Panels . I need to know how to fix this. The zone where the shrubs and tree initially set off the alarm did clear. I am desperate to fix this, and nothing in the manual explains what to do now. The alarm is a C&K systems.inc