Simple troubleshooting step:
Compare the config ('show run') of your working AP to the non-working APs and look for differences the 'dot11 ssid' and 'interface dot11radio 0' parameters. As a general rule, only the ip address, hostname, radio channel and (depending on the environment) power settings should be different on each AP in a small office deployment.
On a side note, the upgrade from vxworks to IOS often results in a lot of unnecessary garbage in the configuration, so often it is a good idea to wipe and reconfigure the APs post-upgrade to clean things up.
-Ben