Ok, it looks pretty much like I suspected
First, I'm wondering whether the actual current is that relevant in this case. The resonance is very sharp and has a reasonable value (not like 0.01), but probably does not change much at all with bias. Therefore, you may not need to spend a lot time computing the current extremely accurately; it seems to me the effect you are looking for is not in the I-V curve but the position of the resonance itself, its height, the difference between spin up/down, how the peak changes when you modify the structure, etc.
The fluctuations in the current are almost certainly due to poor accuracy in the integration. Taking the above point into account, if you are really concerned with the precise value of the current, you need to integrate the transmission spectrum more accurately. However, since the peak is quite sharp, it will be very inefficient to just increase the number of points to a huge value, since most of the points will be in the areas of zero transmission anyway. What you need an adaptive integration routine, that puts more points in the region of the peak, and fewer outside it.
Fortunately for you, I recently wrote such a routine :-)
I'll be happy to share it with you, perhaps, for now, off the Forum, however, since it's not 100% finalized (anyone else who is interested in it are most welcome to contact me!).
However, again: even if you were able to compute the current extremely accurately, I think it will just show a linear increase, which is the bias window "background". The real physics here lies, as I see it, elsewhere, and not in the I-V curve.