I use a Yamaha S90XS, Cubase AI5 and when I add new MIDI tracks I select the new instruments for that track on StudioManager. - Multi mode. 

Usually all works well, all the tracks play and record the correct instrument up to a point, then for some strange reason it seems like the Yamaha and Cubase communication get mixed up because the track will play the 2 instruments together.

Say for example, I have a piano on MIDI track 3 and Piano on StudioManager Multi part3.  Now I add another MIDI track, no 4 and on StudioManager I select strings as the instrument on part4. What happens is track 4 plays strings and piano together on the Yamaha whereas it is supposed to play only strings.  Even I have the part4 (strings) selected on The StudioManager window. And part 1 and 2 still play and record the correct instruments.

I’ve tried taking StudioManager offline and online, turn everything off and close Cubase, restart the Yamaha and restart Cubase but it still happens.

Why does everything work fine at first, and then at some point this confusion happens?

Another thing I noticed is that when I play on the piano keys at the bottom of the StudioManager window, the right instrument plays on the Yamaha, but when I press the keys on my Yamaha it will play 2 instruments together.

For some reason this happens only sometimes, usually I have no problems with the tracks and instruments, correct tracks and instruments for a while and then for some reason I don’t know, the new tracks I add can not play the correct instrument. 

Even if I add more MIDI tracks and set the instruments on the new tracks, it seems to get stuck on playing 2 instruments together.

All MIDI tracks output is set to Yamaha S90XS Port 1. 

I autosync Global and Current when StudioManager starts and use quick setup 1 on StudioManager. The Yamaha is connected to my MacMini with a USB cable.

Any pointers will be greatly appreciated!!

Turn LOCAL CONTROL = OFF on your S90 XS
Local Control determines whether or not your S90 XS keyboard transmit to the internal (Local) tone generator in addition to sending the MIDI data OUT via MIDI. When working with an external sequencer you need to break the LOCAL connection. Let Cubase receive the MIDI data and let the Cubase TRACK “echo” the signal to the appropriate sound device on the selected MIDI channel.

Also get clear in your mind what aTrack is versus what a Part is.

TRACK- only Cubase has Tracks. Tracks transmit data.
Your KEYBOARD transmits MIDI data via a Cubase Track to an S90XS PART
PART- is a Voice assigned to sound when Midi data is received.

With Local Control OFF, your S90 XS keyboard will transmit to the currently active track in Cubase. It will trigger the device and MIDI channel as determined by the Track’s MIDI OUT and CH (channel) settings.

You should double check when you create a new MIDI TRACK, that the MIDI OUT setting “Yamaha S90xs/S70xs-1” and that the data will be routed back to the XS on the MIDI channel you want to trigger.

I’m guessing your MIDI OUT is not the same selection.

Thank you sincerely Bad_Mister, I really appreciate your help.

And having looked back now, it is (admitting red faced)clearly explained on page 19 of the Getting Started manual.I might have lost that setting when I did a factory reset on my Yamaha a few times(my guess).

I struggled with it for so many hours and lost sight of the fact that local must be off. As you can guess, newbie here, learning the hard way and falling into all kinds of traps, but I have only praise for this wonderful software and I love my Yamaha.