The problem happens only when the option "recipe output item multiplier" is activated with the calculations type set to "Total required recipes" thus I highly suspect that the problems lays there.
Ah yes you are right.
This is because iron ore is able to be constructed form 7 different items and overrides the amount mining drones has specified.
You can change 'recipe output type' to default and increase the item multiplier.
Otherwise I can look at adding back in an old feature that let you always keep the highest output instead of overriding with a smaller value.