Hello RoryMac and thank you for the post.
Would it be possible to take this capture again but over a longer time frame? (200ms/div)
Why I ask, yes I can see the flat spots but they seem very sporadic when moving through the waveform buffer, rather than repetitive (in a specific pattern)
The AC ripple itself looks fine can I ask, was the engine speed stable (idle) throughout the capture and do you know if any load was placed across the battery during the capture? (E.g. cooling fan)
Engine speed and battery loading will all effect AC ripple, as will SMART charging systems where charging is often cycled and present when necessary.
If possible on recapture could you monitor Battery DC, Battery AC, Charging Current and any Communication line (SMART charge control) at the alternator.
Here we could see if the flat spots relate to alternator output, battery load or activity on the communication line?