Unless it's out of phase issues or off-axis issues, it's probably the room. Remember that you're hearing more of the room than the source at many frequencies. (i.e., Of the total amount of sound arriving at your listening position, more of it is reflected than direct.) I think every channel sounds tonally different to me during Audessey sweeps even when they're all the same type of speaker. I don't think I've ever had that NOT happen to me.
However, if the difference is extreme enough that it's standing out to you during music playback, perhaps something has gone wrong - driver failure in a speaker or something. Can you put each speaker in one central location in front of you, each in turn, driven by the same single amp channel? And then driven by their own amp channel? If you can control for location, distance, and amp then you can just start going down the list - speaker, cable, amp channel, distance, position....