What am I doing wrong with my camera?

It's driving me nuts. I went to the zoo to takes some photos with my Nikon D7000… Set it on manual and tried for an iso of maybe between 500 and 800 with a slow shutter speed and some middle-ish setting for the f-stop. I get practically a black photo. So just to see what the heck is going on, I set the ISO to the highest setting possible, only slightly better, but insanely grainy. I turned auto iso on and off… Same thing.

It's been driving me nuts lately. I've watched 100s of youtube videos on how to use it, and these should be good enough. I have no idea what I'm doing wrong. I still have my old D80 around, tried it with that one, and it does the exact same thing. I don't remember my manual settings being this bad. Should I bring it to a repair shop or return it or something?

This is one of the photos I took today. It says it was taken at 1/1250 second… But the shutter speed looked and sounded like it was stalling to take it, like as if it were starting a long exposure, then quitting a second later.

Photo - settings on the right.
http://derpingdot.deviantart.com/art/Camera-screwed-up-WTF-is-wrong-with-it-281915303

If you are having the same thing happening on two camera bodies it sounds like it is another problem other than the camera. Are you using the same lens on both?