The current gain in the CE configuration is increased as Vce is increased due to the base width modulation. As Vce is increased, the effective base width is decreased, then, the slope of the minority carriers becomes steeper, then, the velocity of the minority carrier is increased, thus, the collector current is increased.
CE configuration increase voltage and current gain so theres no reason to have negative gain on CE configuation, you have to reanalize more detail about your simulation
regards
Your doubt is right - the current gain of the CE amplifier IS POSITIVE as an increasing/decreasing input current (consequently Ib) causes an increasing/decreasing output current (consequently Ic).
I think you have mixed it up with the voltage gain (CE), which is negative as an increasing/decreasing input voltage (consequently Vbe) causes a decreasing/increasing output voltage (consequently Vce), i.e. phase shift 180 degrees (or PI) between output and input voltages.