Using ethanol bottles in the bio generator causes it to jam up as there is no place for it to eject the empty bottle

after it finishes burning one the other bottles won't burn
I can't get an empty bottle out even if I deconstruct it

That explains it. I thought it strange that it prioritised power from the bio generators sometimes, but not others.

It was ethanol that jammed it up. Good catch.

Also have found that if you use deadlock's loaders to input biomass into the generators, they stop inserting when they get full, and never input unless you reverse the loader direction, when it points back in again, it inserts until full, then stops again.

Next I should try miniloaders or something to see if it's the same... Maybe inserters even do the same thing?

Okay, inserters fill up to 5 and restart when it drops below. Now to try miniloaders.

Miniloaders work just like inserters (no surprise). So it's just the deadlock loaders that stop working.
(edit to fix spelling)

Guys, I removed empty bottles from burnt results of seeds oil and ethanol. But to be fair I increased fuel value of those