For some reason, crops harvested from cropsticks cannot be made into Bio fuel in the mekanism crusher. Things like pumpkin can be placed on the ground and then picked up again and it will work.

Weird. Mechanism must intercept drops in some manner...

Dang it wrong button.

Glowstone dust gathered from glowstone crops doesn't actually stack with glowstone dust dropped from breaking the glowstone blocks, so the crop produce is different in some way,

Inspecting the glowstone dust reveals a slight difference, AgriCraft produce has a compound that vanilla dust does not. The same compound is present on all produce i have inspected so far. The solution i used is running all produce through the mekanism oredictificator, it works.. but not very practical.

Yeah, I've noticed this with a lot of plants, the produce from crops has an NBT tag, whereas if you get the same item from other methods (like potatoes from zombies) then those ones do not have the NBT tag, ergo the two "different" potatoes do not stack.

Thanks for the in-depth investigation! It is very helpful, and I think I should have the issue fixed soon!

This issue has been fixed in the upcoming 2.0.0a11 release.