Assume you tested with the rain bird before switching and all was well. That being the case I would suggest starting with a simple case that was exactly like your rain bird
Unplug your Rachio
Then
Brown on C
Green on 1
Blue on 2
Red on 3
Orange on 4
Yellow on 5
Brown on 6
Leave all rain sensor connections off (label them so you know where they went)
Plug Rachio in and make sure all lights are on. Might take a few minutes.
Test this configuration. If you still have problems then I would suggest that something is not right with the controller and contact support.
If it starts working, then figure out how to incorporate the rain sensor.
Hope that helps
Tom