The belt marks only line up correctly when first installed. To check
if everything is lined up correctly you need to match little dimples on
the three pulleys with marks on the cover. You can do a cam to crank
check with just the top cover off by hand turning the crank to when the
timing mark on the damper/pulley lines up with the "0" on the lower
cover, then check to see that the cam sprocket dimple lines up with the
mark on the top cover. Then you can confirm the secondary shaft timing
by doing a test of ignition timing with a timing light.
Also, most people seem to neglect to reset the timing belt tension 500
miles after a belt change.
Joh