I am facing a similar problem. Most of my results are negative, although this can`t be possible. I already checked the points you mentioned, Andreas: I am not using system expansion (but economic allocation with ecoinvent apos), I set waste treatment to 0, omission is possible but not at that extend, I tried different impact assessment methods ... and results still stay negative.
In my process "sugar production" (FU = 1t) the impact of "sugarbeet production" as an input has opposing positive/negative values than the process sugarbeet production itself (FU 1t), this does not make sense to me at all.
I made a screenshot from the result screen.
I would highly appreciate any help and ideas.