I have a high ALK PHO, GGT, and trygliceride count. What is the cause and am I in any danger?

I have been very helthy most of my life. I am a 42 year old male 260 lbs 6'2" tall. In a recent check up I show
ALK PHO = 154, GGT= 115, and TRYGLICERIDE= 415. I am trying to deploy overseas and was given clearance to deploy. According to 2 different medical professionals I do not have any disqualifing events that would prevent me from doing my job nor to serve my country.

However, when I reported for duty, the base doctor said that he cannot recommend that am deployable unless he knows what my medical condition is.

I reported to him that I had been on the Atkins diet just recently since I am trying to lose weight. He went ahead and dismissed this as a probable cause. In doing some research, I found the following at
http://www.vitaminstohealth.com/atkins-diet-danger.html  in an article titled "Atkins Diet Danger and Risks".

It reads,
"Those with kidney or liver problems face potential atkins diet problems relating to the excessive load the atkins diet places on those organs. Due to the excess acidity caused by ketosis, there is extra work for the kidneys as the urinary system is the primary mechanism the body uses to deal with the ketone bodies produced."

Furthermore, I reported that I had suffered an accident in 2004 were I broke my right shoulder and had kidney stones removed by  lithotripsy  later on that year. In doing some research, I found out that GGT and ALK PHO related to liver and bone disease. Could my prior conditions produce the elevated enzime levels?

Unfortunately, I do not have a lot of confidence in the doctor I am seeing but must deal with him. I have asked him what it is that I have and to tell me exactly what to do but he does not know nor has given me specific instructions.

Could someone please help me? I really don't want to go through a battery of tests to find out nothing is wrong as it has happened to many people in this forum that have had the same problem.

Thank you,

Mr. Sosa