How is your mill frame supported? Is it on wheels, or do you have jackstands on either end? Or is it on fixed posts?
I occasionally have thickness issues when I first set up my portable mill if I don't take the time and level front and back. As the mill head moves over the track, the track may flex. The logs is supported by other parts of the mill, but the head is only supported by it's posts. When it gets near the ends it may track lower in relation to the cant, and that's how you end up with differing heights from front to back.
I don't think you have a blade issue, either with alignment or sharpness. Unless you can run your hand over the board and "feel" waviness in the cut, your blade is probably not the problem.
One other thing is that cant's move while they're being sawn. IF the log has "reaction wood" in it, and it's not secured by the posts and clamps, it may react as you cut the board from it. I don't think this is your problem though. If it were happening, you'd notice the board that you cut flexing up or down as you cut it.
I think the frame / rail supports are where you will find the problem.