Lakshman
Champion
Champion

In addition to pbjork post, ThinApp always sets 'WriteCopy' isolation to the below folders, irrespective of 'Merged' or 'WriteCopy' isolation is selected during setup capture.

%AppData%
%Common AppData%
%Local AppData%
%Program Files Common%
%ProgramFilesDir%
%SystemRoot%
%SystemSystem%
Similarly, ThinApp always sets 'Merged' isolation to these folders irrespective of any isolation mode selected during setup capture.
%Desktop%
%Personal%
%SystemSystem%\spool

Hope this helps.