The way power is calculated will and does produce negative values when the direction of power flow reverses.
So my first guess is, you are not measuring the current where the power does indeed reverse. So where are you measuring the current? Is it really where you think it is? It must be between where your service entrance wires enter your property, and the point where the PV infeed is connected.
My second guess is you might have connected the a.c. reference voltage after you powered up your emonPi. If you did, it’s decided it hasn’t got an a.c. voltage input, and it’s ignoring it. Then it estimates apparent power using the nominal voltage, and that will never be negative. The solution to that is power down your emonPi (a reset is not good enough) and power up with the a.c. input connected.
