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Ian,

Two things to think about that may lead to a solution to your stitching
problem.  I am by no means an expert but have had the same problem - though
not with a coolscan. Your scanner lamp changes as it warms up. The scanner
sensor should compensate for this but it may not be doing it. Possibly you
could let the scanner warm up longer.  The other thought is to save the
negative to positive conversion data from the first scan and use it for the
second half. 

AZ

ps I couldn't get this message to reply to panorama list so i sent it direct
to you