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I think it has something to do with the matter/anti-matter reactions and subsequent creation of the electo-plasma. It seems as if when the warp drive is off-line or running at a low rate, the plasma inside is pink. When the engine is running, it turns the blue, which is also the color of the plasma that leaks from the nacelles during venting.

When you kick plasma up into the terawatt range, it colorimetrically turns from pink to bluish-white ProfessorTrek 10:04, July 29, 2011 (UTC)

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