iTunes + Arduino = problem?

Its general 'good advice' to let Disk Utility's First Aid do a 'Verify Permissions' on your disk before (and for the paranoid, after) doing any install/upgrade/update/reinstall. (Do a Repair Permissions if there's any problem found - or just do that first without the preliminary Verify.)

Its a matter of cleaning up before and after potentially sloppy installer programmers, rather than a system thing.
Just a safe habit to develop!