Janeway also promoted Torres to full lieutenant after initially granting her a Lt. j.g. status, in the first few episodes of season 1, after Chakotay whined and Carey groaned.
Unfortunately, we don't know for sure how this went. Torres wore a very ambiguous set of dashes on her collar during the first season: it seemed to be one dark dash before the promotion to Chief Engineer in "Parallax", but in subsequent episodes, at times both the dashes appeared dark and at times one or even both seemed dark.
The standard insignia settled on one bright, one black (Lieutenant jg) from the second season on, and it was made explicit in "Day of Honor" that Junior Lieutenant Torres indeed was outranked by Junior Lieutenant Paris (who had had the 1½ pips slightly longer).
For logic's sake, we could argue that our TV sets were playing tricks with the color of her dashes. Before the "Parallax" promotion, the single dash would have been dark (enlisted rate); afterwards, the two dashes could have been bright (Lieutenant) or possibly one bright, one dark (Lieutenant jg); and after the mutiny in "Prime Factors", if she had worn two bright dashes, one would now become dark.
Timo Saloniemi