I was in the military for 16 years--the moves and TDYs were constant. Didn't really have time for a long term committed relationship, before one or the other of you was transferred or sent TDY for a year. But other than getting tired of losing one partner after another, I had no problems like what you describe.
As a master's level counseling clinician though, I'd be more inclined to believe it might have been a physical guilt reaction, based on your upbringing or even societal pressure. Sometimes you just don't know what's lurking around down there in your unconscious mind.
While it's better than it used to be, there's still the whole stigma and shaming thing about not behaving 'properly' as a woman.