Hi,
Let me understand the following,
1. What controllers (Model -3600/3400/3200/72XX etc..) you are using ? and which AOS(6.1/6.3/6.4 etc..) you are using ?
2. Do you have sufficient AP license installed (show license ) on the Controller
3. How these APs are getting IP address
4. What Master discovery method you are using ?
5. If possible please share the output of "show ap database"
Please comeback with the above, we can fix the issue easily :)