altura, when you switch on your S-series keyboard many of the buttons (like UNDO, QUANTIZE, AUTO,...etc) are not lit. This is normal.
If everything is installed correctly then - upon starting Reaper - these buttons will get illuminated.
Q1: Can you please confirm if the buttons get illuminated when you start Reaper?
If they do not get lit you have an issue with the detection of the keyboard and/or the NIHIA drivers. As per manual:
Troubleshooting if your keyboard does not get detected after launching Reaper:
* The keyboard must be switched on before starting Reaper.
* The NIHostIntegrationAgent Service must be running. If in doubt check it in Windows Task Manager and restart the service.
* The MIDI Device name must be exactly “Komplete Kontrol DAW - 1”.
* Do not rename the dll filename.
Q2: You stated that you got transport control working. Did you use MCU control surface to do that? If so, don't. You cannot have both MCU and NI's deep integration protocol running.
If you suspect that you have some USB port issues you may also want to restart NIHardwareService. Try in the following order:
1. switch off keyboard
2. restart NIHardwareService
3. restart NIHostIntegrationAgent
4. switch on the keyboard
5. start Reaper