I am using connman for wifi connection and it is controlled over dbus. The system supports many wifi connections. The user can remove and add a connection.

If there are saved connections and wifi is currently disconnected and connman is asked over dbus to do a scan it falls into the scan on channels retrieved from the saved services.
So user sees only APs on these channels.

There is a commit which addressed a similar issue but when there is an active connection

There is a ticket https://01.org/jira/browse/CM-602 which describes similar symptoms but a different root cause. 

The patch forces wifi device do a simple scan if the scan is originated over dbus. In this case wpa_supplicant will do a scan on all channels.

Best wishes, Volodymyr Ostap