Andy -
Those are excellent suggestions and comments. I did some tests yesterday having removed a haze filter which I was using for element protection only but it had definitely created a mild vigneting that was adding to the problem.
The problem still persists, but now exactly along the lines you have described - very subtle, but problementic, upon closer examination usually entails both a density shift and a chromatic shift, usually along the cyan/red or magenta green axis. It's not predictable - i.e. of a six shot panorama, the third shot may be out or the fifth.
I spent several hours on the phone with Canon yesterday (yes, pray for me) - the only useful bit of information was an insistence that I use center weight metering instead of evaluative. I explained that I was shootin in full manual (shutter, aperature, custom white balance, etc) and the tech insisted that even in full manual the metering capacity of the camera is "sending impulses to the sensor" - can this possibly be true?

I have downloaded a trial version of Stiticher and - weird Euro interface aside - seems like an interesting program anad I will be exporing it more.
I do not have any info on the Canon shutter issue but will look into it.
I should add on top of all this that my EF 24-105 mm F4L lens is subject to recall - whether or not that's contributing to the problem, will advise.
thanks for your thoughts - durt