toomany is probably correct, the black co-ax wire is probably for a cell phone. I think the other end of the black wire is near the glove box. I've never bothered to follow it all the way back. You should be able to ignore it.

The factory antenna wire is the grey co-ax just above the black wire in pic 1. It attaches to the 'fork' in the antenna in the top center in the same pic. The other end of the grey co-ax wire is behind the radio in the console.

If both ends of the grey co-ax are connected to radio and antenna, respectively, then the problem 'might' be poor connections between the aluminum collar, the antenna mast, and/or the ground. I think that collar with the antenna port is a slip fitting, so make sure that it's snug on the aluminum tube that connects it to the motor housing (or it might be theaded, so maybe try loosening the set screw, then spinning the tube to see if it tightens into place). Then make sure the set screw that holds the tube in place is tight (enough to hold the tube in place but not super torqued down) then make sure the motor is ground to the frame by both the brown bundle and the antenna bracket itself.

I'd also plug/unplug the grey co-ax behind the radio a few times to loosen any possible corrosion at that end.

Pic 3 is a dry-fit pic and does not show the grey co-ax connected, but you can see where it would go in pic 2. The metal tube running sideways across the pictures is the sunroof teleflex cable housing. Try to leave this alone if you're messing with your antenna.