The flash is not in sync with my nikon d40 anymore. It fires first. Pictures come out dark. The camera itself takes great flash pictures

It sounds like you're trying to use the SB-600 off camera, as a slave flash. While the SB-600 does indeed have slave capability, the D40 does not have the ability to function as a commander. Thus, the SB-600 is being triggered by the D40's pre-flash.

As stated above, the D40 does not function in commander mode. You can mount an SB-800 or SB-900 flash unit, which will function as a commander as well as a flash. Or you can mount an SU-800 commander unit.

Alternatively, you can switch the D40 to manual flash mode so as to eliminiate the preflash. However, you will then have to calculate the proper exposure yourself.