Here are several ideas...
Okay, first of all you wrote you are seeing the same issues with both lenses: 17-40 and a 50mm.
Which 50mm? If it's the 50/1.8, it's a micro motor lens with a reputation for somewhat iffy auto focus. Many folks who try to Micro Focus Adjust it eventually give up, because it isn't very consistent. It also tends to hunt a lot in lower light. You probably would see better results with only the center point and this lens, but a USM lens such as the EF 50/1.4 or similar would give much faster, more consistent AF.
The 17-40 is an f4 lens... so can't take full advantage of the f2.8 sensitivity of the center AF point. Still, as an USM lens, it should focus more surely and quickly than the EF 50/1.8.
What focus mode are you using? One Shot or AI Servo?
See the AF point pattern in the above response? Note the 6 points right around the center one (roughly on or within the circle denoting the spot focus area), making for a total of 15? Those are "hidden" Assist Points that have to be enabled in the menu, are not indicated in the viewfinder and only work in AI Servo focus mode. The other nine points (center one, plus 8 peripheral), as seen indicated in the viewfinder, are available in both One Shot and AI Servo. For the type of photography you are doing, I'd be using One Shot, which gives greater accuracy than AI Servo. (Notes: 1. Above ignores AI Focus mode... because it really isn't a focus mode at all. In AI Focus the camera is supposed to decide for you whether or not the subject is moving, then switch to using the appropriate mode: AI Servo for moving and One Shot for stationary subjects. 2. Live View focusing uses contrast detection AF instead of phase detection that's done with the AF points seen in the viewfinder, is even more accurate than One Shot, although it's much slower.)
Of the nine "usual" AF points, on 5DII (and 5D original for that matter), yes, only the center one is the more sensitive "cross" type. All the others are single axis an less sensitive. However, for the types of things you shoot, they should all be usable. The 5DII's AF system is rated down to about -.5 or -1.0 EV light levels, if memory serves. I find the center point on mine is actually a little better in low light than my 7Ds or, before them, 50Ds... all of which are rated the same as the 5DII. Slower, yes, but still able to lock on after the 7Ds and 50Ds gave up completely.
Anyway, I most often use the center point only on my 5DII (and with other cameras). You do have to be a bit careful focusing and recomposing, though, with any shallow depth of field shots.
Regarding calibrating your lenses using MFA... I haven't used the product you mention and don't know how you are using it.. Canon and Reikan Focal both recommend the "target" for most lenses be at a distance 50X the focal lenght of the lens. So a 50mm lens would have a target 2500mm or 2.5 meters (or about 8 feet) away. A zoom lens is harder to MFA.... you probably should check it at both extremes of the focal length range and if they aren't the same (seldom are) might need to arrive at an average amount of adjustment or skew it a little toward one end or the other that you use most. (Note: newer cameras with a later version of the MFA feature allow for two adjustments to zoom lenses, one at each end of the zoom range.)
Also, I've heard of folks having trouble doing calibration indoors, in artificial light. In particular, any common fluorescent lamps can mess with AF. Best if possible to do it outdoors in sunlight or light overcast or light shade.
Stopping down to f11, you should get a lot of depth of field that would hide most minor focus errors, unless the subject is very close (i.e., near macro distances).
If the camera and lenses haven't been used much, you might try cleaning the lens to camera electronic contacts. I recommend just lightly dampening a clean, lint free rag with a few drops of isopropyl (rubbing) alcohol and carefully wiping the contacts with that. There might be finger oils or something on them effecting AF performance.
It also might be worth having the camera cleaned. Perhaps some dust has settled on the AF sensor array or on the mirror that's effecting AF performance. I don't recommend trying to clean these yourself, perhaps aside from a puff of air from a bulb blower.
How are you viewing and evaluating your images? I ask because many people make the mistake of over magnifying images.... looking at a 5DII's image at 100% is like looking at a five or six foot wide print from 18" away... so close that minor and meaningless flaws are bound to be seen. I usually evaluate image focus and sharpness at 50% or 33% with my cameras (though I do work on images at higher magnifications for other reasons).
Also, some softwares can be a little "flaky". I use Lightroom extensively and have to be careful. When I open an image at even moderate magnifications in the Develop module, it takes a while to load, showing an enlarged thumbnail intially that always looks poorly focused... And I find if I have the crop tool active, it takes even a little longer to render the image correctly and show it's true sharpness and focus accuracy.
Finally... do you have any filters on the lenses? If so, try some tests without any filters. I have seen filters effect AF performance. If not using one it's possible a lens hood might help, too, by keeping oblique light off the front of the lens.
All that being said, it is possible something is wrong with the camera and you should have it (and the lenses) looked at.
Hope this helps! Keep us posted.
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Alan Myers
San Jose, Calif., USA
"Walk softly and carry a big lens."
GEAR: 5DII, 7D(x2), 50D(x3), some other cameras, various lenses & accessories
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