questions:
1) is the fence flat? a reasonable straight edge should suffice for now.
If so, then:
2) just to clarify, does the fence lock down parallel to the blade and move?
or:
3) is it "toed in" toward the blade when locked down (but doesn't move)?
sounds like #3 from your description.
Before proceeding, it is absolutely essential that the blade is parallel to the miter slot. Have you done this?
Assuming you've made the blade to miter slot parallel check, here's my 2 cents on the fence. From the manual you have 3 adjustment mechanisms.
The first regulates the tension of the locked down fence. The fence should move smoothly when unlocked, so back out this nut until it just moves smoothly. Then check that when locked down the fence doesn't move at either end. If it's too tight, you may run the risk of slightly deforming/torquing the fence. If it's a newer craftsman I'm guessing that aluminum is quite thin and flexible.
The 2nd adjustment makes the fence 90 degrees to the table. Check this with a good square. Typically I'll back the screws out until they're not registering, then tighten until they just register, and begin tweaking until I'm satisfied w/ the adjustment.
The third adjustment sounds like you're problem and is a common adjustment for a T-fence. Again, back these screws out so that they do not impede sliding of the unlocked fence and begin tweaking until the fence is parallel to the front and back of the blade. The key is how to determine this. I use a jig from John White's book Care and Repair of Shop Machines. It's a board about 10-12" long and 2-3" wide with a dial indicator mounted on it. This slides along the fence. The other jig is a piece of 3/4" plywood 10" x 2 1/2". Drill a 5/8" inch hole (size of your arbor) about an 1 1/4" from the end. Mount this board onto the arbor and rotate it all the way to the front of the saw. Now, with the fence locked down close enough that the indicator will register on the board mounted on the arbor, slide the board toward the front of the saw as far forward as posslble while it still makes contact w/ the arbor mounted board. Zero the indicator and mark the spot on the board. Now rotate the board toward the back of the saw, slide the jig down the fence and re-measure at the same spot. Adjust the screws on the front of the fence slowly until this measurement is < 0.001". Should be good to go. I'd also highly recommend John White's book for setting up other machines. Also, sorry if these measures were already taken and your problem still persists.
HTH,
Sam