I was launching my first three comm satellites for remotetech and was having one heck of a time stabilizing my rocket. I ended up having to place the jumbo airliner wings on as fins, since nothing else was effective enough, and even then, the fairing was producing more lift than the four wings at certain angles/speeds/altitudes. I removed the fairing at one point, but the top stack had so much drag, the effect was essentially the same with or without.
I spent days trying to figure out the issue. I t took some time to finally narrow it down to the fairing, but once I did, I was able to adjust it for a stable flight.
My fairing's length was the problem. I started it about 2/3 up the rocket. The fairing was straight for most of it's length, and only bowed out and around the package slightly before closing to a very nice aerodynamic point on top. It made sure the tip was streamlined, as I have noticed that blunted fairings fly like bricks.
I did not touch the bulb of the fairing at the top. What I did was moved the fairing higher up, as high as I could get it, so it was as short as possible. The bulb and cone were the same, I only removed the straight sections of fairing that were below it. The rocket beneath those sections were just fuel tanks and standard modules, nothing that needed a fairing, but I liked the look of the longer fairing, so that's why I used it in the first place. I didn't think the straight section below the bulb was going to have that much of an affect on the craft.
Well, after shortening the fairing to just the essential bulb and cone, my rocket nearly flew itself in a perfect gravity turn. I still needed the giant wings on the back to compensate for the fairing and the length of the rocket, but removing that unnecessary length was what ultimately solved my stability problems.
I went through everything trying to figure out why my rocket would flip. CoM, CoT, CoL, velocity, AoA, length of the rocket, TWR, attached and re-attached just about everything that could drag or hang in flight, test, retetst, reretest.... ugh..
TL;DR: Shorter fairings are best. If you need one, make it as short as possible.
As an aside, has anyone tested whether where you click above the rocket to close the fairing is being used as the topmost point, and if possibly closing the fairing by clicking on the actual visual tip would be a way to workaround the bug? It seems like that might be what's happening, but it'd require some rigid testing to be sure, which, without a testing facility like a wind tunnel, means flight is the only option.