I believe Dandi may be right. I've seen this before and dug out this piece by Dr. Andrew Weil which elaborates in a bit more detail:
Do Low-Carb Diets Cause Bad Breath?
I've had noticeable bad breath lately. Someone told me my high-protein, low-carb diet is to blame. True?
Answer (Published 2/4/2005)
True. Bad breath (halitosis) is an unfortunate side effect of low-carbohydrate diets. Here's what happens: the diet causes your body to burn stored fats for fuel rather than carbohydrates. As the fat burns, chemicals called ketones build up in the body and are released through the breath and urine. Unfortunately, they're smelly.
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There's not a whole lot you can do about bad breath that stems from the way you're burning fat. If you're determined to stay on the diet, you'll just have to put up with the halitosis. Dentists say that extra brushing, flossing and tongue-scraping won't help because in this case bad breath isn't an oral hygiene issue. (The Atkins Diet Web site acknowledges that bad breath is part and parcel of the way you're eating and puts a positive spin on it, saying that it means that the diet is working.) Some dentists have speculated that the other popular low-carb diet, South Beach, may not be as problematic, since it permits more carbs than Atkins.
The best you can do to cover up the bad breath associated with low-carb diets is to drink lots of water, which will also wash away food particles that may be contributing to the problem. Chewing parsley is another way to address halitosis. Sugarless gum or mints may also help mask your breath, but I'm not a fan of the non-nutritive sweeteners they contain.
I'm also not a proponent of the Atkins diet, so I would suggest switching to another program that allows you to eat fresh fruits, a wider range of vegetables, and whole grains. This is a more realistic way to lose weight in the long-run since you're likely to get tired of low-carb living sooner or later and regain whatever weight you've lost.
If your halitosis persists after you go off your low-carb diet, see your physician. Bad breath can be a sign of diabetes, sinusitis, gastroesophageal reflux disease (GERD), and a number of other medical or dental problems.
Andrew Weil, M.D."
"I will work in my own way, according to the light that is in me." - Lydia Maria Child