Hi,
just a guess...
Most other vendors use LLDP for topology discovery.
Cisco by default uses CDP.
Did you enable LLDP on your cisco switches?
If not, then your ciscoes do not see the APs as their neighbors. Not sure if the APs list the ciscoes.
At least Aruba/Procurve switches listen to cdp by default and add this information to their lldp based topology tables.
So, enable LLDP globally and enable lldp tx/rx on all interfaces and give it a try.
Kind regards, Jörg