I agree with Zeddhead that the tool rest - the long bar and its mounting - is the prime suspect.
I don't have a genuine Tormek, I have a Dakota one*. Those tool rests (identical to Jet et al, too) have exactly the same problem - cheapskateness - only a threaded nut on one shaft, not both. So I have a process that works:
1. Check the side of the wheel is running true (disengage drive shaft by taking the rubber-tyred wheel off & check wobble with something like a pencil clamped in the tool rest). If this is wrong you're stuffed as you can't do the rest of the process!
2. Check rim of wheel is square to the side (engineer's square).
3. Set tool rest bar to also be square to the side.
4. If necessary, true-up wheel with diamond thingy.
Then you're good to go (and apart from (4) that lot takes longer to read than to do, honestly).
I have a couple of "Smoothcut" Japanese laminated plane irons, and although they're really, really wonderful, THEY TAPER slightly across the width. So you can't trust the indexing blocks on the plane iron holder and have to eyeball it. I often end up with the skew lever on my planes pushed quite far over, but it's not the end of the world - as long as I end up with a good finish (and squareness) life is way too short to lose sleep over the squareness of the pointy end.
I take Jacob's point, but the same machine gets used for all sorts of things from chisels through to the garden shears, electrical screwdrivers (which I am fairly anal about being square and true, and yes I can square-up those!) and kitchen scissors. My hands shake sometimes; I have trouble holding certain shapes of object, and having a Tormek-style jigged system takes out a lot of the potential for cock-ups.
It's only a slow grinder though - I have once or twice succeeded in getting chisels dry-shave sharp with it, but not consistently, so I use it for re-grinding, not for final honing. I don't love it, I just use it - a tool to help do what for me is an awkward job otherwise.
E.
* "My name is Eric and I have been a Rutlands Customer." (sits back down in the ring of chairs, to half-hearted applause).