It sounds like Induction Flu, but if it doesn't calm down in a few days, go see your doctor.
Are you eating every few hours or so? Drinking the required amount of water? Are your carbs extremely low? Some folks say they feel better when their carb intake is closer to the 20, so check yourself out at fitday.com. Here's a link to explain how fitday can help you.
(Fitday!)http://www.atkinsdietbulletinboard.com/forums/showthread.php?t=5235
You may also want to post a menu in the Review my Menu forum so we can have a look at it. Take a sec to read the sticky in there on how to post your menu. Including the time of day when you eat is helpful as well.
I know I felt like the dog's breakfast still on day 7, with headache, lethargy, body aches...the whole shebang...but hang in there and it should pass.