My 5d Mark II won't show focus properly through the viewfinder but can with liveview?

I absentmindedly let my 5D Mark II jostle around a little today and now when looking through the viewfinder it's seemingly not focusing properly, yet when pressing the shutter button it shoots the photo in perfect focus as long as I focus it correctly in the first place. When I switch it to liveview mode, it also focuses fine. I'm also hearing a weird noise when it's shutting down, but this could just be placebo considering I haven't had it for all that long and just may have never heard the noise before. Could this be an issue with the viewfinder picking up the focused image, or the camera itself is having an issue?

When the camera performs it's self-cleaning it uses a piezoelectric effect to "vibrate" a filter located in front of the sensor (when you look at a "sensor" inside the camera you area really looking at a filter in front of the sensor... dirt and dust would actually be on the filter -- nothing is able to touch the sensor itself.)
Also... the focus screen on the 5D II is replaceable with optional focus screens.  The focus screen is a frosted screen which rests in a tray (a frame).  The back of the frame is hinged.  The front clips in to the top of the camera.  
See:  http://www.learn.usa.canon.com/app/pdfs/quickguides/CDLC_FocusingScreens_QuickGuide.pdf
This may have come loose and your focus screen may not be firmly closed (and this woudl change the focus distance ... resulting in your not being able to see a focused image when looking through the viewfinder and could even account for the rattling noise.)
It is very important that you NOT actually "touch" the focus screen trying to close it.  It is difficult to clean without damaging it and finger oils from touching would be a problem.  Also the cameras metering system is above the screen and smudges can affect the accuracy of the camera metering system.  For this reason, those optional focus screens actually come with a tool included to help you swap screens without ever needing to touch it.
Canon's tools works a bit like a pair of tweezers ... except with a hook on the end.  As you just need to verify that it's locked up in place, you can use something to push the tab up so that you don't have to do this with your fingers.  A popsicle stick, a chopstick, etc. would all work to "close" it, etc. but the tray has a tiny tab which normally needs to be gently pulled toward you to release and lower the screen... but usually just pushing upward (without pulling) will allow it to "snap" back into it's clip.
Here's a video demonstrating how the focus screen compartment is opened and closed.  You can check to make sure yours is closed.  This CPN video demonstrates using a 40D but the operation is identical on your 5D II.
Tim Campbell
5D II, 5D III, 60Da

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