FishEye/Crucible 2.2 onwards, scheduled backup directory could only be changed via /FISHEYE_INST/config.xml.
To do so, add <path>backup_directory</path> right after the <schedule...> element.

<backup><schedule enabled="true"><path>C:\backup</path><prefix>....

Kindly include the above info for

• http://confluence.atlassian.com/display/CRUCIBLE/Backing+Up+and+Restoring+Crucible+Data#BackingUpandRestoringCrucibleData-SchedulingCrucibleBackups
• http://confluence.atlassian.com/display/FISHEYE/Backing+Up+and+Restoring+FishEye+Data#BackingUpandRestoringFishEyeData-SchedulingFishEyeBackups