I ran into an issue this season using a lithium battery with my Flow Pro controller. Lithium batteries are around 13-14.4 volts. The Flow Pro control board wants to see around 12 volts so the signal with the higher volts was intermittent/spotty.
The fix was installing a DC-DC buck-boost converter between the battery and the Flow Pro to provide a steady, regulated 12 volts.
The converter I found (amazon) is rated for 8–40V DC input, regulated 12V DC output, 10 amps, and is waterproof. Since it’s a buck-boost converter, it can regulate the voltage up or down.
Both the positive and negative wires need to run through the converter, with an inline fuse on the positive side. The converter powers the Flow Pro controller and actuator circuit directly from the battery (from the distribution posts in my setup).
Anybody else who runs into this problem hopefully finds this thread and can get themselves a buck boost converter to solve the issue. I like the storage capacity of my lithium batteries and I definitely wanted to keep them. I ran this idea by Jud who gave me the go ahead. Best to everybody, hope the season is going great for you 
