I think it's a result of the fact that they just weren't sure what to do with her character. In the pitot she wore a Uhura-esque uniform. Then they decided to play up her counselor/captains advisor role and make her more like a civilian. Then, as was pointed out by others, they started going back to Troi being a Starfleet officer. I'm betting in some meetings they realized that taking her out of uniform had been a mistake but were unsure how to fix it. Jellico was an easy way to do that.
I like her better in uniform, but I'm a girl. Star Trek has never been above sexing up the women for ratings (watch how Kira's uniform changes over the years on DS9 and of course theres Seven)