Strange things can happen when you put a boost converter (external), a 5volt buck converter (Due), and a linear 3.3volt regulator (Due MCU) in series.
Both switching regulators probably have UVL (under voltage lockout). The Due has.
And likely high startup currents, that the generator might not be able to supply on startup.
I don't see this working without some sort of battery/charging system.
Leo..