I have the same behaviour, it shows as "False" in the search result view. But if you open a single user and go to the "Component View" tab, Wireless message reconciliation shows "Enabled" there, so it is really a display issue.
It seems to be a known issue. From the release notes
BlackBerry Administration Service known issues - Release Notes - BlackBerry Enterprise Server for IBM Lotus Domino - 5.0.3
After a BlackBerry device user sets the Wireless Reconciliation option to Yes on a device running BlackBerry® 6, the change is not synchronized to the BlackBerry Enterprise Server and the BlackBerry Administration Service displays the status of Wireless Message Reconciliation as False. (DT 1033792)