This really doesn't make sense to me. Which is why I am asking about the crank keyway. I've seen it get funky on others. Unlike the HB key, the crank key would cause that exact problem because then things wouldn't be timed properly.
One of the things I love about the 3.8 is that it's nearly the worlds simplest motor. Set balance shaft to cam, set the cam key to about 4 oclock, crank key to about 2 oclock and presto, your nearly timed right. Then the HB and sensors take care of the rest. Crank goes around twice and the cam once. So by lining up the dot you put the intake lobe in the right place. Degreeing is a good idea and it has a lot of merit. However it would be off a slight amount, not enough to bend rods like pretzels.