I do this all the time - reorder images to force a particular area as 
dominant while stitching - with Hugin on Windows.  

The current version [2011.4, used last week in exactly this fashion] and 
previous versions going back as far as whatever was current in 2004-5 [I 
have done this with every version available since then] have all worked 
correctly for this, for me.  

Not sure what to suggest to you, Darius.

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