There is additional memory overhead involved with crossfire. There were some graphs of GTAV running with decent averages and mins with a single 290 and much higher averages and very low mins on 2xCF (via 295x2). I don't know how much it is but it exists. Now, I'm not saying that is the case here. There is not evidence to say one way or the other without more specific testing. It is certainly possible if the game is right on the precipice of 4GB.
An easy test to help zero in would be 2x 4GB 390's now that they exist vs 2x 8GB 390s and see what happens.