Awin, thanks again for the detailed reply - your patience and help is MUCH appreciated.
So, some more detail... the 50mm is the cheapie 1.8 (yes, I'm on a budget). But even with that said, I really wouldn't expect such glaring inconsistencies in sequential photos. Check the following full resolution samples (and note, all three are sequence photos, with a good pause between shots for reacquiring focus)...
thanks for sharing your photos... as neuro mentioned, it does appear to be severely front focused however i'm not sure about your options regarding the tokina lens. If there is any consolation prize, you can live with it, call it art, and charge 3x the price =). I used to have quite a selection of sigma lenses once I started upgrading my gear from the 10D to 30D... Once I moved to the 50D I joined CPS and still am with CPS. Ever since then I only have 1 sigma lens left (10-20mm) which I will keep until I make the leap into full frame completely. The reason I did that was in the long run, if i needed anything fixed within canon, it's just one company to deal with than sigma (and or tokina, tamron, etc)... If you have a full MA and you still cant get + or - 20 something doesn't seem right. IF and that's a big IF it is the case and there is a severe incompatibility, I would ask if you still have your 40D and if it still works great with the 40D. If you got rid of the 40D, just asking, but is there a chance it was dropped or something happened to maybe loosen an element to cause it to be so far off? Just trying to rule that situation out.
Regarding the 50mm 1.8, I cant say I've used that lens so I cant speak for that lens... From what reviews i read, it was a good bang for your buck lens with the 1.4 and 1.2 being just a tad sharper overall which speaks a lot for a lens averaging just about $100. The 1.4 is a good lens, however in another forum post, i gave my 2 cents on that lens... It's sharp from 1.8 and up... however the crappy micro usm causes me to almost wait a second or two to allow the lens to fully catch up to me shooting which is ok for portraits, so-so for event photography, however for fast shooting, is a nightmare. It's a lens issue for that lens. Also the focus mech for the 1.2 I tested left me wanting a lot (A LOT) more. I dont know if the 1.8 issue is because you're shooting to fast (not fully waiting on the focus beep) like my 1.4 has or if it is a MA issue. That's one of those hands on things I couldn't tell ya unless i'm there. As far as upgrading, i would wait and see if and when the 1.4 gets replaced. Then I'd buy one once they are out and reviews come back glowing.
You mentioned you sent in your camera again... I hope you sent all your lenses in because I would hate for the adjustments they made last time to make the 28-135 and the other lens to get screwed up just to make the 50mm up to par. As always, if you have any more questions or concerns, feel free to email me or post a message for me.