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I ran into similar issues shooting hockey, also with a 70-200 non-IS, a 30D and also a 40D. I shot over low glass near the bench, so the glass wasn't a variable. I even sent the lens and the 40D to Canon because of the problem, and they both came back as OK within spec.
Frankly the problem continued until I upgraded to a 7D, when things improved, and then I finally tried a microadjustment, and things got even better.
In your case you may have an easier situation for Canon to fix, since it seems like your issues started after the Err99 service. I decided I was dealing with the low-light AI Servo limitations of the xxD cameras, and maybe some indifference from Canon but admittedly with a problem that might not have been easy for them to reproduce.
Does your camera also back focus in good light, maybe shooting soccer? Mine didn't, which was another reason I decided the low light played a major role.