Like VXorado said, I think the marks on the crank and cam pulley's should be in the same position on every rotation, but that does not mean that they will line up with the marks on the belt every time (if that makes any sense). Just due to the way things are rotating, and the length of the belt, the marks on the belt won't always line up with the marks on the pulley's.

I seem to remember mine doing that when I replaced the timing belt. Marks on the pulley's always ended up in the same place after every rotation, but not necessarily lined up with the marks on the belt.

PM Bart to see if he remembers anything.