Just got my new camera and couldn't figger out how to get manual exposures to work, so I used auto settings until I had time to read the manual thouroughly. Having done that, I did not find a solution to the problem. When I'm on manual, it seems that the mirror sticks up... all of the auto settings are working fine, though, so it's not a mechanical problem. This happens with a large variety of lenses that I use with my D60.
Another problem is that I prefer to shoot RAW but it occasionally reverts to JPG without me consciously changing it. This is just strange.
First go into your menu settings "Clear all settings". Than set the dial on the left side to 'M'. Now turn the small wheel on the right top and the big wheel on the back for adjustment.
You may have put the camera in 'silent shooting', too. More likely than live View mode.
Yep, 666, that's what's made me so lucky in finding people with the solutions to my problems:-)
However, I still have no idea how it changed from RAW to JPG... I often lay it down uncased, so buttons could have been pushed without my knowledge, but that seems pretty unlikely that that particular combination could have been accessed.