By default, the CRM 4.0 Re-Indexing and Deletion jobs are scheduled to run every 24 hours. Unfortunately, the start time for these jobs defaults to the time of day when they were originally installed on your server, typically sometime during regular business hours.
To avoid any potential performance impact that might result from these jobs competing with users for resources, they can be scheduled to run during the night, when few, if any users would be affected.
To set the time and/or frequency of these processes, use the ScaleGroupJobUpdate tool from Microsoft support.
Download the tool to the CRM Server desktop and start it by double-clicking on ScaleGroupJobUpdate.exe. ( You’ll need to be CRM administrator with access to the CRM application server to use the tool.)
(If you’re hosting more than one CRM organization, make sure set the tool to the correct organization.)
Choose the Job Type “Deletion Service” and set the “Base Time” to the time of day you would like the job to run – then click Update. (The base time is the time of day the jobs will attempt to run each day if scheduled to run every 24 hours.)
Change the Job Type to “Re-Indexing Service” and again set the base time and click update.
The default interval for both jobs is 1440 Minutes (24 hours) – this can be adjusted for one or both jobs if needed.
Additionally, by setting the “Job Next Run”, you can effectively run these jobs ‘on-demand’ (i.e. Re-index records after a large data import or run the deletion service after a significant number of records are deleted to perform a ‘hard-delete’ of those records.)
As always – please review the instructions and information on Microsoft’s site before using the tool in your environment.
Thanks to Scott Sewell for the tip - http://blog.customereffective.com