If you guys follow my wallpaper thread, you can sometimes notice what OP has brought up. Most of the time, I just lack the patience to equalize the colours - it takes too much time and ultimately I don't think that a variation in shades is a very big problem -, so I usually put those characters in red (or yellow) uniform in different wallpapers for the same episode.
But yes, it is true that most of the time, even within one episode there's a noticeable difference in the shades of the same uniform colour. Most of the time it is the lighting although sometimes the fact that not every (original) screencap can be of the same quality accounts for this. I don't know if you've noticed that Voyager gets way too many scenes (compared with DS9 for example) where the lighting is less than sufficient so this makes making pictures difficult not only because of the various shades but also because you can hardly see the characters in a lot of scenes at all! Voyager obviously finds herself more often than not in a "red alert" situation or for some other reason they have to decrease the intensity of the lighting so colours change dramatically. Take EQUINOX, for example. This is an episode I would really like to start making wallpapers for but nearly two thirds of the episode takes place in the dark so this will be a tough one.
It is also true that even within an episode with zero to little variation in the intensity of lighting, the colours can display different shades. This is often due to the fact that the actors are lit from different angles or if they are lit from the same angle, then one of them is standing further away from the lighting point and the shade of the uniform slightly changes. But sometimes, this has simply to do with the fact that a character's uniform is creased (in a battle or something) more than that of other characters so the shade again changes very quickly.
So all in all, I think it's a safe bet that colour is a sensitive thing and you can't always get it perfect in every scene.
At the same time, I would really be interested to know if the actors had more than just one uniform. I remember Robert Duncan McNeill once saying that his first memory re VOY is always that as the show progressed, the uniforms had to be adjusted every season (I guess they were gaining weight - maybe gaining and losing weight) so I automatically assumed that every actor had just one uniform that had to be adjusted. But then they wore those uniforms so often that maybe they needed a whole set of them - if that was the case, then it further complicates the problem of the uniform colour.