@netguy - Here are my answers:
1- Multiple commons - not unusual. Wired correctly in Rachio.
2 - Same color field wire - seen it before on posts. Makes it challenging, but so it is.
3 - P to M - correct. Whether a pump start relay or a master valve - it needs to be turned on with the zones. Hunter labeled it P, Rachio labeled it M.
Possible solutions (a few too many variables to discuss them all):
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Swap M and 5 wires - if they were mis-wired and the master valve is currently in zone 5 that could be the reason why only that zone works.
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An educated guess is that the second common wire may go to just to zone 5. Is zone five in a different area? If this is the case then there may be a break in the common wire after the master valve. If the master valve has a dedicated common wire and zone 5 is closest to the controller it still could be a break in the common wire after zone 5. To test one will need an ohm meter. Disconnect the wires from the Rachio and test the resistivity down a zone line and back to a common line. If there is no resistivity on one common line try the other. Resistivity should be in the 25 - 30 ohm range.