In the above pic the one on the left is not aligned properly. The one on the Right is aligned correctly.
In the blow up of your pic the Green Arrow indicates the Direction of Rotation.
The Purple Arrow Indicates 10 degrees before Top Dead Center (10 degrees advanced)
The Red Arrow points to Zero Degrees = Top Dead Center
The Yellow Arrows point to 10 degrees and 20 degrees After Top Dead Center and this is Late/Retarded Timing.
I would try Rotating the Engine again and being extremely careful aligning the marks. I mean get you Eye right up next to the marks because if you are lookiing downward on it or at any sort of an angle it will throw the alignment off.