Hello,
Do you mean the hardware combination system is not working or the Hauptwerk combination system? You can always test everything in Hauptwerk by using a mouse to set pistons then click on them to make sure they have presets captured. If the virtual pistons are working properly when using a mouse but not with your hardware then it would point to either you having incorrect settings in the switch MIDI inputs menu, or incorrect wiring of the hardware itself.
Make sure that you know what type of MIDI messages your hardware is sending by either consulting the documentation for your hardware, or using MIDI OX or even Hauptwerk built in MIDI logging function to monitor the incoming MIDI data, then have a look at the tutorials page for setting up switches at http://www.hauptwerk.com/tutorials.
The transposer being set at 0 just means that notes are not transposed, so that is normal and is the default setting. The transposer doesn't relate to getting sound output, it just affects the pitch of the sound by adjusting the MIDI note number inputs to play however many steps up or down you have the transposer set to.