Randy Ulmer says that FOC DOES affect trajectory.

This from Randy Ulmer:

"Your arrow’s balance point will affect its trajectory – at least slightly. For example, an arrow that is “tip light” will remain a little more level in flight and will actually plane or sail along a flatter trajectory than one of the same weight but with a heavier nose. But, tip light arrows don’t correct quite as fast when they come out of the bow. The closer the center of gravity gets to the physical center of the arrow the less stable the arrow will be in flight. A slashing arrow pivots around its center of mass (balance point). The farther the balance point is from the fletchings the more leverage they have and the quicker they can bring the arrow back on line.

The experts at Easton feel that an FOC value that is between 10 and 15 percent will produce the best compromise between stability and a flat trajectory for most hunting situations. The American Society for Testing and Materials have published a procedure for measuring balance point, and in it they state that a value of 9% is typical. But, they also add that the range can be as wide as 7% to 18% while still producing good arrow flight. 3-D shooters seeking a flatter trajectory often go a little lighter on the nose with many shooting arrows having FOC balance points closer to 6 percent. "

http://www.randyulmer.com/archive/2007/02/07/arrow-stability/