One thing you can try is to run the firmware in command line and see if there is any error message printed out. To do so, first follow instructions here:
to stop the firmware from running automatically. Then go to the folder where the firmware is installed (e.g. /home/pi/OpenSprinkler-Firmware), and run
This will launch the firmware in command line, where you can see debugging messages. When you start a program or manually start a zone, see if there is any error message that could be related.