I've just gone over the screencaps, and there are some shots where the nacelles are illuminated when the ship is at relative rest, e.g.:
http://movies.trekcore.com/gallery/albums/tmp/themotionpicture0860.jpg
Judging from the screencaps, I suspect the illumination indicates that the warp engines are functional and online, not necessarily that they're in actual use.
http://movies.trekcore.com/gallery/albums/tmp/themotionpicture0860.jpg
Judging from the screencaps, I suspect the illumination indicates that the warp engines are functional and online, not necessarily that they're in actual use.