After a couple of days trying to have a successful packet transference using the radio module from Microchip, the solution ended up being related with the initialization of the device.
In the protocol we are using is not needed to use the Extended 64bits address, just the 16bits address is enough, therefore in the initialization routine of the MRF24J40 the registers associeted with the extended address were never written.
The problem appeared when the packages transmitted from the coordinator were decrypted successfully but not when the communication was from the End Device.
It seems the security engine of the radio module needs a value in the extended address fields. it was the solution, in the inicialitation of the device, now there is a value being written.