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I'm using an Canon 1Ds mk II with the focusing screen "Ec-D: Laser-matte with grid" that has a grid dividing the screen both horizontally and vertically. Lighting up the focus points clearly shows that the focus points are shifted slightly to the right vertically. The shift is only in the order of about a quarter of the length of a single focus point indicating rectangle.

I've not had any problems with the focusing system, but since I've not used the camera with symmetrical alignment I can't be absolutely sure.

I can see a couple of reasons for this. The focusing screen could have been incorrectly installed, the focusing indicators can be projected slightly wrong or there could be some issues with the actual focusing system. Is any of the above more likely or lies the problem elsewhere?

Is it likely to cause any problems and if so how can I correct it?

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Actually, the focus points that are displayed in the viewfinder are only a somewhat rough approximation of where the actual focus points in the guts of the camera are located and how big they are. Consider it as the camera telling you that "focusing will be done somewhere in the vicinity of this bright red square thingy" and you get the right idea. So I'd not worry about this at all if I were you. Considering all the other slop that is involved in the phase detection autofocus process in an SLR, this is a very minor thing.

Incorrect installation of the matte screen (focus screen) or installation of a "wrong" (i.e. unsupported on your particular camera) matte has absolutely zero impact on the camera's autofocus system. It may throw the light-metering off a bit, that is all. There is a sub-mirror behind the partly-transparent center section of the main mirror in the camera, this reflects light down into the bottom of the camera where the AF sensors live. This light is never even near the matte screen. The light-metering on the other hand is done up in the mirror house, which is why an odd or exotic matte screen can affect metering because the light being metered has already passed through and been affected by the matte screen and the metering system has to know about and compensate for this.

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    \$\begingroup\$ Until you focus manually... then focusing screen misalignment becomes critical. \$\endgroup\$
    – Michael C
    Commented May 13, 2014 at 3:21
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It's worth noting that even the focus point LEDs can be off the mark and may not accurately show where the focus really is. Knowing this, you can see why it'd be hard to say what problems a misalignment of focus screen and point indicators will give.

Most likely, if there is any issue, it'd be that the focus point you're expecting to be in sharp focus is out a little. But of course if the LED is also out you risk pulling out your hair to find the issue. I know my dSLR focus slightly out of alignment with the focus point indicators and I've got used to it.

As to it being corrected, you could always ship it back to the manufacturer and have them look at it ($$$), have the focus screen re-seated/replaced to see if this improves things, or live with it. If it's a minor misalignment I'd be tempted to live with it. If it niggles you a lot then it's probably worth spending some cash on it to get it fixed.

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