Hey everyone...
When I started atkins (a little over a year ago) I went through something similar. Did you give up coffee or caffeine? Many people feel extremely nauseous and kind of ill from caffeine withdrawal. This did happen to me and I caved in and started drinking coffee (limited amounts) again. The coffee did not keep me out of ketosis and helped a lot with my queasy stomach.

Also, I agree with an earlier post here: are you sure you are drinking enough water? I don't care what anyone else says, for me it is essential to drink almost 100 ounces a day. The water really flushes you out. Anyways, good luck and I hope you feel better!
Jenn