When I installed my cam, I had the engine on a stand with heads off, and used a dial indicator to find top dead center as accurately as I could. Once I found TDC on the #1 cylinder, I made marks between the rear flange of the crankshaft and the back of the block. Later, when I went to install the harmonic damper, I verified that #1 was at TDC, and that the timing marks were properly aligned with the timing indicator. They aligned perfectly. I'm using a Romac Balancer on a Ford 5.0L Stroker.
The factory balancers have a rubber ring between the hub and the outer ring where the timing marks are located. The rubber fails and then the outer ring slips relative to the center hub. After that the timing marks are arbitrarily located and no longer consistent.
Long story short: Find and verify TDC, and make sure the balancer marks can't slip.