Yep, I bet the gas block is mis-aligned.
As far as indexing it properly, this is the technique I have used with success:
Use a straight edge to make a mechanical pencil mark on the gas block seat from the gas port all the way to the shoulder of the seat. If you picture the barrel as a globe, this will mark the "longitudinal" position of the barrel gas port.
Now place the very edge of the gas block so that it half-way covers the gas port opening in the barrel. Tighten one set screw to hold the block in place, then using the mechanical pencil circumscribe the barrel using the edge of the gas block as your stencil. This will now give you the "latitudinal" axis of the gas port's position on the barrel.
Next, make a mark on the face of the gas block indicating the position of the gas block gas hole. If you are going to dimple the barrel, after lining up your "longitudinal" mark on the barrel with the mark on the gas block face, you can now look through the rear set screw hole for the latitudinal pencil "ring" mark you've just created on the barrel and mark the spot for dimpling. Of course, you will want to tighten it down verify that its positioned correctly by blowing air from the muzzle end of the barrel while plugging the chamber (with something like a mop, patches, etc). Look listen and feel for air movement.
OF COURSE, this technique assumes that your rear set-screw hole and the gas port opening in the gas block index EXACTLY (or sure as hell close-to) 180 degrees from each other. If they don't, then the above won't work.