Terry, Preferences can be managed at three levels within Windchill. The Site admin can set these at the top level driving the settings to every context. An organization admin can set preferences at a context level...ie a user checking out from a jet engine product context would get different settings than checking out from the fastener library context. As a third option, the user can set preferences under the quick links drop down if the applicable setting is not locked by the site admin or organization admin. I believe the site admin can "push" out settings to users to override their personal preferences too...but don't quote me on that one.
It also depends on which area of Windchill you are using to check out the objects. There are more than 6 areas within the UI where you can check out or add to workspace. I'll list 6 of them here - Embedded browser connected to Creo - workspace table, Search results table or Information table on the object. Then you can get the same three options in a non-embedded browser - workspace, search and information page. If you are performing the checkout from different UI's, then be aware that the settings may not stick when switching workspaces in the dropdown menu if you have multiple workspaces in different contexts. (A case was entered for this a couple months ago).