I am wondering, if by "bowed" you're saying that when you set the barrel on the flat that shows a space between the barrel and the flat surface, when the opposite is placed on the flat surface, it shows that the barrel will rock somewhere in the middle of it's length, or if it shows the same void between the flat and the surface. it might be that you have a swamped profile barrel. check all eight sides to see if it might be swamped. you might have gotten a swamped barrel by mistake.
another possibility is that the barrel has been straightened. this process is done by looking at shadows in the bore and bending the blank after it is bored, so that regardless of what the outside shows, the bore inside the blank, is straight. if the bow isn't all that noticeable by just holding out and looking at it, you might try indexing the bow in the vertical plane when you set the barrel in the stock. this isn't necessarily "correct", because there should be no bow, but if the barrel can't be replaced for some reason, it is a remedy, given the bore is straight in it's currently bowed condition. that said, I would first contact Green Mountain and tell them you'd like to return that barrel. and of course, as Kutter said, you can always file the barrel to produce a tapered barrel that compensates for the bow. don't forget to file the central area of the barrel opposite the end you file to make the barrel have straight taper. I would also not trust the counter top to be absolutely straight. I spent my working career fabricating counter tops and installing them, and I can tell you assuredly, there are very few, if any,.... that are actually dead straight.
