I had the same thing.. it lasted for 2 months. From what I understand it is normally and there is nothing much you can do about it. It started around 3 weeks for me as well.
Here is the scope on ketosis thanks to wikipedia
(Now I could be wrong this might not be what you are going through but in my case this is what it was and it did go away. )
Ketosis
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Ketosis (IPA pronunciation: [ki'tosɪs]) was identified by Dr. Stephen Moody in 1969 and is a stage in metabolism occurring when the liver converts fat into fatty acids and ketone bodies which can be used by the body for energy.
When glycogen stores are not available in the cells (glycogen is primarily created when carbohydrates such as starch and sugar are consumed in the diet), fat (triacylglycerol) is cleaved to give 3 fatty acid chains and 1 glycerol molecule in a process called lipolysis. Most of the body is able to utilize fatty acids as an alternative source of energy in a process where fatty acid chains are cleaved to form acetyl-CoA, which can then be fed into the Krebs Cycle. During this process a high concentration of glucagon is present in the serum and this inactivates glucose kinase causing most cells in the body to use fatty acids as their primary energy source. At the same time, glucose is synthesized in the liver from lactic acid, glucogenic amino acids, and glycerol, in a process called gluconeogenesis. This glucose is used exclusively for energy by cells such as neurons and red blood cells.
Ketone bodies, from the breakdown of fatty acids to acetyl groups, are also produced during this state, and are burned throughout the body. Excess ketone bodies are excreted in the breath and urine. The brain has a residual need for glucose, because ketones can only provide energy when used during aerobic respiration in mitochondria. In the long thin neurons, much of the metabolically active cellular membrane must derive its energy from glucose via anaerobic respiration without the assistance of mitochondria.
If the diet is changed from a highly glycemic diet to a diet that does not substantially contribute to blood glucose, the body goes through a set of stages to enter ketosis. During the initial stages of this process the adult brain does not burn ketones, however the newborn brain makes immediate use of this important substrate for lipid synthesis in the brain. After about 48 hours of this process, the adult brain starts burning ketones in order to more directly utilize the energy from the fat stores that are being depended upon, and to reserve the glucose only for its absolute needs, thus avoiding the depletion of the body's protein store in the muscles.
Ketosis should not be confused with ketoacidosis, which is severe ketosis causing the pH of the blood to drop below 7.2. Ketoacidosis is a medical condition usually caused by diabetes and accompanied by dehydration, hyperglycemia, ketonuria and increased levels of glucagon. The high glucagon, low insulin serum levels signals the body to produce more glucose via gluconeogenesis, glycogenolysis and ketogenesis. High levels of glucose causes the failure of tubular reabsorption in the kidneys, causing water to leak into the tubules in a process called osmotic diuresis, causing dehydration and further exacerbating the acidosis.
Most medical resources regard ketosis as a pathological state associated with chronic starvation. Glucose is regarded as the preferred energy source for all cells in the body with ketosis being regarded as a crisis reaction of the body to a lack of essential carbohydrates in the diet. In recent years this viewpoint, both the body's preference for glucose and the dangers associated with ketosis, has been challenged by some doctors.[1][2][3]
Whether ketosis takes place can be checked by using special urine test strips such as Ketostix.
Deliberately induced ketosis through a low-carbohydrate diet has been used to treat medical conditions although most such treatments remain controversial.[4] [5] The ketogenic diet is an approach to treating epilepsy, and the Atkins Nutritional Approach (and many similar diets) is marketed for treating obesity. The very low calorie, medically supervised Lighter Life and Lindora diets also use ketosis for weight loss
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