Have you made sure that the Microfreak is set to receive on the MIDI channel that the DJS track is transmitting on?
It is pretty safe to assume, that unless you have altered the Microfreak's settings, that it is set to receive on MIDI Channel 1.
On the DJS, by default, each Track, if its type is switched to MIDI, will transmit MIDI note data on the channel with the same number as the Track. So DJS-1000 Track 13, for example, will transmit on MIDI channel 13.
If you have changed a DJS-1000 Track type to "MIDI" and you are in the TRACK MENU, you will see the "SELECT CH" button. There you can manually enter what MIDI channel (between 1-16) that track will send note data on. Make sure that Track is sending on the MIDI channel that Microfreak is set to receive on. Also make sure that DJS-1000 Track isn't muted.
Did that solve it?