When you start manual watering, did you received a notification "Starts in -- mins"? It is possible that you Pixie timer is in sleep mode.
By default, your Pixie turns on its WiFi module once every hour to sync up with the server. The sync-up usually takes less than one minute. For the next 59 minutes the timer will be sleeping and disconnected from the WiFi until the next sync. When the timer is sleeping, it is unaware of the schedule changes, including the manual watering.
Therefore, when you start a manual run, the timer is most likely in sleep mode and the status is "pending." It will have to wait until the next sync-up to start the watering.