Nikon D90, put it on manual but it still automatically sets settings

Okay, so i photographed at a friend's dance recital, and at one point, i switched my 18-200 lens for my 50 mm film camera's manual focus lens. I eventually switched it back to the 18-200, but ever since, every time i put the camera on manual, it keeps automatically changing the shutter and aperture for me. I have no idea what's going on with it! Please help!

Added (1). It is most definetly on autofocus and on manual. I double checked, i even tried taking out the lens and putting it in again. But its the same.

Are you sure you have the camera in the manual exposure mode? What you are describing sounds like you have it in the program mode.

With the camera set to manual, as you move the lens aperture, you will see the light meter indicator in the view finder move either + or -.

Is it the focus or the exposure that's on Manual?

Read page 83 of the user manual.

Remove the lens, then re-install it.