Hi Darren,
None of the livery generation code touches the Alternator 2 logic, so imagine this is some coincidence in testing. The Alternator 2 on the SR22 needs a few requirements to be met to engage:
The Essential bus must be powered to engage the field protection circuit. (This can be powered by Bat 1, Bat 2, or Alt 1)
The RPM must be relatively high, due to the circuitry of the setup (>~1500-1750 rpm)
There is a timeout on the warning, so I am guessing it only gets noticed after running the livery generator due to the time it takes.