I cannot give you data on what will be asked as I have no idea. However, I agree with LAsam818 in that you already have established yourself with a fine military career. In my opinion, the concern about prostitutes is not that they don't like somebody who would do this, but rather that it could be held over your head in the future. For example, one of these madams could eventually say "do me this favor Mr. FBI agent, or I will tell your wife about our trysts." It's far fetched, but still a concern. I am also ex military and had a secret clearance. Honestly, I don't want anything to do with this kind of stuff anymore. You may be happier becoming a "complete" civilian and live your life without all this externally induced paranoia.

Truth be told, I dont think your chances with the FBI are good cuz of the prostitutes and can even mess up your military career. Normally I would say "take the risk, what do you have to lose?" but I see military service as something that most wouldnt want to risk. 
In some cases, yes it does automatically disqualify you and it may black ball you.

A little about myself first. I am military 4 years with a top secret clearance and a masters degree. Never been in trouble with the law and smoked pot less than 10 times in high school and college. I plan on applying for a govt job when I get out of the military possibly FBI. Now for my question.

Since I have been in the military I have had sex with a few prostitutes on Craigs list. I Plan on being completely honest with my answers on the polygraph.

1. Does the FBI ask questions with their polygraph on past sexual behavior, and if the do what do they ask?

2. Does having sex with prostitutes automatically disqualify you from getting a job within a FBI or any govt job that requires taking a polygraph?

3. If I do take the polygraph and disqualified for my past sexual behavior will that black ball me from most govt jobs?

I would really appreciate some good feed back on my question. Thanks.