Hi,
I just wanted to chime in, because I think this is still an issue.
My nuclear reactor consumes uranium rods and produces spent MOX.
The situation was the following:
I have a mixed input belt with uranium rods and mox. The internal storage was full with mox and uranium rods. The reactor continued to consume only mox (which is what I want), so the internal storage went down, which is expected behaviour, because I think the storage of 80 is actually dedicated 40 mox and 40 uranium rods.
So the storage went down to 40/80 because the next item on input belt was a uranium rod, but the uranium storage was full, so nothing made it into the reactor.
Now the following accured:
The mox rods went down to zero, but the mox recipe still went on. But now it consumed uranium rods (still showing the mox recipe being active) and it output spent mox, regardless whether a mox or a uranium rod was consumed.
Below a few screenshots to maybe help illustrate the issue:
Only 1 mox rod left:

last mox rod being consumed:

consuming uranium rods and outputting spent mox (see belt)

After a reload of the map and deactivating the mox recipe, it still woudn't work as expected:

Maybe important: The reactor startet up on uranium rods producing spent fuel (the yellow one), and after putting mox fuel in it, it still was producing spent fuel, but consuming mox, so the exact opposite of what my issue is now. It somehow fixed itself, can't tell you why or how though, sorry :/
UPDATE: After another reload of the map, everything functions properly. You can even see the switching between the fuels in the UI. Mox gets consumed whenever a rod is available, otherwise a uranium rod gets consumed. Just how it should be :) The produced waste is also correct.
UPDATE 2: After a pause and unpause of the game, it's broken again. Sorry for the updates.