Scaling gone a stray? So I scaled the top part like so.

Now all of the sudden whenever I try to scale it does this.

It seems like scaling it is just moving it now, also when I hit "S" to scale and then type in 0 it just shoots to the bottom of the mesh. 

Please help me brothers.
Probably your scale center is the 3D cursor.

Scaling and other operations are dependent to the center of it.

You can change that from the options shown in the picture below.

For what you want, probably "median point" is the good choice.