I'm gonna go with electrical issue.
Did you test batteries under load?
Have someone crank the engine, and test voltage on each battery while cranking.
Should not drop below 12 volts.
A starter solenoid will partially engage, but not fully if voltage is low. They can click, click, click in rapid succession without engaging.
Fuel solenoid is smaller, so won't need as much current, but the same could be happening.
Assuming you have used the 12 Volt/24 volt start system?
your theory that one battery being low could effect voltage at the solenoid might be right.
With the 12/24 volt system, the batteries are connected in parallel, so both running 12 Volt systems. On start up, the connection is altered so they get linked in series to provide 24 volts to the starter only.
I'm not certain, but you may see a momentary drop in voltage in the 12 Volt system if the left side battery (primary battery) is weak.