Are you sure you are looking at the right marks?
I did what what you are doing a few months back and had the passenger valve cover off to check for stretch. I rotated the motor by hand until the cam marks lined up and to my surprise, the 180 mark was staring me in the face. After a few seconds of panic, I rotated the rest of the half turn and another cam mark appeared and lined up exactly on 0.
The balancer is impossible to put on wrong unless you re-drill a new hole-so that's not likely to be the problem.