When the furnace runs fuel with Acceleration value it seem to become a different entity, rather than merely applying a virual module bonus.
The consequence of that, is that "Allowed fuel" list, is not the same as the base entity.

Example, you can feed an idle furnace Krastorio2 Bio fuel kanister just fine, but as soon as it start runing the fuel will be deleted due to not being on the list.

Bizzare inconsistency, it sems not all fuels (including vanilla items) cause it, And some of the fuels that should be expluded by the change, do not trigger the change.

Thanks for the report. Furnaces with an acceleration bonus are indeed a different entity, but they are supposed to copy the allowed fuel list from the base entity.

To help me reproduce this, which mods are you getting "idle furnace" and "Krastorio Bio fuel kanister" from?

Idle furnace just means a furnace that isn't working at the time, because the change only occurs when the furnace is runing, and then comes back to normal once its done. i tried it with the two vanilla furnaces and they worked the same.
As for krastorio bio fuel Canister... the item name is "bioFuel", which is from Krastorio2 mod, the icon for which looks like a Canister (not sure which spelling is correct)

Other than some quality of life mods, I Only run with Krastorio2 and Space Exploration being the only big mods.
Also Deadlocks stacking beltboxes, but that only adds stacked versions of smaller items, not modify anything.

Thanks, I was able to reproduce it. It is a conflict in data-final-fixes.lua, where Krastorio adds new stuff after this mod has already run.

I asked Krastor to move the changes earlier in the loading stage. If that is not possible I can add a dependency to ensure this mod loads last.

Fixed in version 0.18.1.