Since you've done it before I won't try to suggest what is wrong, but answer your question as you've put it. Which to trust? Trust the motor. Wherever the reference marks are they form a straight line through the cam and crank shafts. The whole thing looks lopsided because the motor is tilted in the compartment, but trust me, the line from cam gear index to crank gear index intersects both shaft's centers.

If you doubt the marks on the belt, count the belt's teeth, starting #1 at the cam index, #45 at the i-shaft index, and #72 at the crank index where the double line is.
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-K (hope springs eternal)