Solved. Finally the problem was caused by a stupid configuration but I think some thoughts could be interesting por somebody:
The problem was an incorrect configuration of the default system profile. Despite of the fact the AP was properly whitelisted, with an assigned AP-group that was properly configured, together with its system profile, the default system profile was wrong. This caused the AP was assigned to a default AP group and the AP travelled to 'nowhere'. Possible improvement: If there were some message, either on the AP console side, either on the controller side logs, informing about the assigned lms controller, this problem could be easily solved, because, in my opinion, there is not enough information to guess what was happening or, at least, not easily accesible.
Other thinking about this issue: The system profile configuration was wrong because this controller's connectivity had been reconfigured. The problematic APs were associated at a first moment to this controller (besides the bad configuration), but at a later moment, the provisioned AP database was deleted. This probably caused the assignment to the default system profile on booting. Logs indicating a first discovery of an access point, not explicitily provisiones would be appreciated.