In some cases, a filter is placed on a system field to limit the choices a user can make. Organization, for example. In situations where only certain organizations should be visible remove the search magnifying glass so the user can only select one of the values provided in the filter.
Have the same issue with an 'Approver' person field...initial search is limited to a list of approvers only, but when the advanced search is used via the magnifying glass it pulls up role-defined, nit field-defined search results.