If you check the timing with a light and it idicates the timing is correct then my GUESS is that the timing is Correct and you must not only have the cm geaar marks that are off but also the crank must have moved as well.
In short this means that all the gears would be off a couple notches and the timing is correct by the light.
It would be hard to prove as the crank mark is blocked by the pulley and timing cover.
It the belt must have moved on the crank too. While you were trying to get the others lined up.
Looks like if one cam is on with the distibutor and the crank then the timing willshow on but 1 cam will be off. THANKS NEO
Good Luck!