Set Data Sources not working

Hello,

I am trying to change the geodatabase source for all but two layer files in my MXD file. I am using the Set Data Sources.. tool in the ArcCatalog tab. I select and change the layers in question and their new source is shown in the tool. I click save, and then open the newly created MXD to find that none of the sources have changed.

Could there be something i'm doing wrong? or is this a known issue?

I am running ArcGis for Desktop Basic 10.1.

Thanks
Michael