My cross shafts do have more than one index, for what reason I don't know because if you put your steering arm on the wrong index mark there is no way that you can get it into the tie rod and have it even close to centered. To say it another way, there's more than one mark on the cross shaft but if you use the wrong one, you'll know it right away.
You know, when I first put mine back in, I did slip the steering column on about 2 teeth off, I noticed it before I snugged everything down and corrected it. I know you said you checked it but the mark on my coupling was not very accurate.
If your saying that everything else is straight then why don't you just slip the steering column off and move it to the left about 2 teeth. ( I hope I'm understanding you correctly, I'd hate to be confusing the issue even more.)