"Uppity" is a synonym of arrogant, presumptuous.
Scattered throughout the Voyager series (probably after the first couple of seasons), Janeway would take an air of arrogance or presumptuousness. Also, tending to make emotional outbursts, unfitting of a captain. I don't have Voyager episodes memorized, so I can't just point to evidence all throughout the series... but I know I've seen it. I think part of it is the difficulty of playing a woman in that role and still keeping it interesting. In the real world, commanding officers have to project a certain persona to get the job done, regardless of gender. I think Mulgrew wanted to give a more feminine character to her role... and it's understandable, because most people watching the show aren't in the military and wouldn't understand a realistic representation. But you have to be careful not to take things too far. I didn't like her portrayal in Equinox, and yet she was superb in "Year of Hell". Nobody pulls off a role perfectly. Mulgrew did some great work... but yeah, the "uppity" could have been toned down a bit.