Thank you for your patience.
Well, some good news and some bad news.
The bad news is yes, the SP16 does not send CC#0 or CC#32 to trigger scene and pattern changes, respectively, to the DJS1000. Additionally, as you have observed, the Bank Select function works but you have been triggering it manually. As you may have noticed, the "MSB" value tells the DJS1000 which Scene to pull up, and the "LSB" value instructs the DJS1000 to call up a certain pattern.
The good news is that the Bank Select function is actually automatically sent...but only when loading up that Scene in SP16...not when changing to any particular pattern. This is because the MIDI Track will always have the same Bank Change value across all patterns within a Scene.
But, as you know, each Scene has an entirely new setup of 16 Tracks. So each Scene can send out a Bank Select message when it's loaded. So if you have a MIDI track which has a Bank Select value locked in at, for example: 002, 005 (Scene 3, Pattern 6)...that Bank Select message will get transmitted to DJS1000.
When the DJS1000 receives that message, it will cue up the Scene and Pattern corresponding to the Bank Select message it has just recieved from SP16...but the actual Scene and Pattern switch may occur 1 bar behind the SP16 if the machines are both running...so keep that in mind.
So, while these changes might be better off if done manually, you CAN get the DJS1000 to select a scene when you select one on SP16.
Hope that helps,
Devon aka Rhythm Droid