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                It is possible to set the temp folder.
Follow the link and there is a section called Changing the location of the temporary files.
http://www.red-gate.com/supportcenter/content/SQL_Data_Compare/knowledgebase/getting_better_performance
Hope this helps. - 
                
                  
                
                Thanks for the fast response - yes it worked perfectly 
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Database are only small - just under 5GB