Your question is far from clear, so I'll have to guess.
The indication is that you're sending midi data via USB from the computer to the Yamaha, but it would be helpful to know where the midi data is coming from. Are you playing a midi file? Where is the midi file from, and what do you know about the data in it?
The midi data may or may not include 'patch' settings, that set specific channels to specific instruments. The data in the file merely selects program nn, and may be using a GM (General Midi) number. The Yamaha may NOT be set for GM, and may be responding to the command and selecting the correct number, which could be NOT the instrument you want/expect.
There could also be problems with the actual channel selected, The Yamaha may not be responding on the expected channel. You do not say if the sounds you hear play JUST the wrong instrument, or are playing the correct instrument AND a wrong one (so multiple channels may be active (unexpectedly ?))
If you are playing a midi file, if you could 'zip' it and attach, then I can look at the data and confirm just what is there. Some midi data might include NO patch/program settings, as a setup might have been assumed, but your Yamaha DOES need something?
The more/better info you can provide, the more helpful I can be.