It sounds like you are running the RPi independently of the control board (the board accepts 24VAC and provides voltage regulated power to the RPi attached). If this is the case, I’ve had a few situations on other projects where I could see the LED boot indicator lights activate but not get a good bootup. I found that the supposed one amp power supply I was using did not provide enough power. I swapped to a known good unit and was able to boot. Not sure if this is your exact problem, but something to try in your troubleshooting. Good luck.
PS – the interval program (python based irrigation control app) included in the image from the base documentation is out of date. Make sure you update it to the latest before investing too much configuration time.