AF issues with 5D (Mark 1)

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When I noticed that my hardly used (but more than 12 months old!) EF 50/2.5 macro had uneven sharpness across the frame at 2.5 at wide apertures, I sent it off to be reset. I tested it on return at all apertures (raw, on tripod, MLU, viewed at 100% on screen), one set on AF one-shot and a second set manually focussed. The manually focussed shots are noticeably better at 2.5 and just detectably at 4.0. (I really need to do this test with all my lenses but haven't the time right now.) Does this point to a focussing error with the body? It occurred to me that if I sent the body off for recalibration, against what would it be measured? Without the benefit of AF calibration for each lens/body combo (which of course is available if/when I get a 5D2) I could easily get the AF reset but it could actually be worse, not better?

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