I know this is an ancient thread, but wanted to add a bit.
As Eric can attest, I've been fighting alignment issues since day one. Things just never cut right. I've added a Forrest dampener, PALS alignment, shimmed the living %#$ out of my fence, and things were still sloppy.
And now I figured out why.
When everything seems perfectly aligned and nothing works right, something is wrong in the equation. For a saw, everything is based upon one reference point - the miter slot. Usually guaranteed straight, mine turned out to be a boomerang of fail. Maybe the previous owner sanded or ground or wore it out somehow, but blade and fence alignment for the left slot versus the right were night and day. Now on the right slot there's only a few inches of shimming tape for the fence and it cuts like a champ. The other downside is that I need to get this one out the door asap before my upgrade comes (but that's for another gloat thread). To top that off, I'll get to re-align my crosscut sled and every other jig I have.
So my point is, trust but verify. A TS-Aligner is great, but don't base your readings off of one alignment point if possible.