If I'm not mistaken, once you turn the engine the match marks will be out of line. This doesn't indicate a problem as the match marks are only used when putting the chain on.

To double-check the timing:
1. Turn engine to TDC mark (0 or Top):

2. Double check the alignment of the shaft marks (the dowel hole and the key groove in the diagram). If you are careful, you can tell if it is a tooth off, or not. Use a level or a t-square or some other precision straightedge as an tool to make sure they line up -- exactly.