1) In the TNG Companion, they confirm that Ro was making a veiled reference to Chakotay.
2) Tuvok was a lieutenant in the early days of Voyager yet wore lieutenant commander pips. Then they fixed the pips to reflect his rank of lieutenant. THEN he was promoted to lieutenant commander not long afterward. Yeah, you'd think he was demoted but the events were so far apart that it makes no sense.
3) Finally, I always interpreted Chakotay's rank in "Caretaker" to be commander as in he's the guy in charge of the fuckin' ship, hence the reason the Maquis all called him commander. Didn't have anything to do with rank; the maquis didn't care about ranks. So Janeway made him a commander and her XO. Yeah, Cavit was a lieutenant commander too, but that has nothing to do with Chakotay.
I'm affraid that I must refer back to Chakotay's rank pips and references available at http://www.startrek.com/startrek/view/series/VOY/character/1112391.html and http://www.memory-alpha.org/en/wiki/Chakotay. "Following the destruction of the Val Jean in the Delta Quadrant, Chakotay and his crew joined Voyager's crew.
Chakotay was granted the provisional rank of lieutenant commander] and became Voyager's first officer. Chakotay accepted Kathryn Janeway as captain, and embraced Starfleet ways. : "Caretaker")
Any way theres no indication that Janeway promoted him above his last held Starfleet rank. It's common for first officers to hold the rank of Lt. Commander. Picard picked "A Young Lt. Commander" to be his first officer, and Captain Janeways original first officer was a Lt. Cmdr. Now, I always beleived he was a full Commander until recently... That's one of the reasons I started this thread, to get to the bottom of it. I don't know if we ever really will know but on screen I can't recall him ever being refered to as "Lt. Commander". We do know it's common for Starfleet Lt. Commanders to be refered to as "Commander." See any episode with Data, LaForge, or Worf in DS9.
Let's not forget the season one rank errors with both Tuvok and Paris.
Yet another Voyager mystery.
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