Error in setting permissions:The permissions were set correctly. Here I found the solution.
Operation not permitted [chmod(/media/storage...
Unison stores sync profiles in ~/.unison/*.prf. Edit the relevant prf file, and add a line 'perms = 0' and it will always ignore permissions for that profile.
See also the unison documentation: http://www.cis.upenn.edu/~bcpierce/u....html#profiles