Thought I would bring this up in case anyone else has the same issue.
I've been using a 12 year old Irritrol controller for my 4 zone sprinkler system. Moving to the Rachio was a no-brainer since I wanted more control with my phone.
Right after I installed the Rachio, two out of the four zones stopped working. I then removed the Rachio and hooked up the old controller. The two broken zones still did not work.
After doing some troubleshooting I discovered that the solenoids for those two zones ceased to function after I installed the Rachio. My thinking is that they were on the verge of failing anyway and the Rachio simply pushed them over the edge.
So, to make a long story short, after checking the wiring and making sure everything is configured correctly, you might want to check the solenoids as well especially if they are very old. Replacing solenoids is easy and takes less than 5 minutes. YouTube videos will show the actual procedure. Should only cost about $8. It's worth a try especially if all other attempted fixes are failing.