An update has been posted in the myspleen comments section. It seems the color was indeed off and a corrected version will be released in the future.
Man, and those guys were defending their transfer hard.
[quote]Because of the amount of people complaining about some of the scenes being too yellow, and the Youtube clip posted by one of the users we started wondering if the color is right ourselves. Unfortunately, it was revealed that there has been a huge misunderstanding between the person who did the scan and the one working on color correction. I won’t get into details, but a whole movie color grading is wrong and does not reflect the look of the print.
Some of the scenes need minor corrections (these are most likely the ones that made me think the whole scan is right, I haven’t screened the entire print), but others, like the dojo fight or Neo’s interrogation are completely wrong. The movie will get a shot by shot color correction in the next months, if you wish to watch a theatrically accurate version of The Matrix, please wait for the new version (it will be labeled v1.5).[/quote]