Hello wjoefox,
First of all, have you followed the instructions in the 'Quick-start: stand-alone' section of the user guide (on the Help menu in Hauptwerk; starts on page 44 in the current v3.30 version of the guide) to select the correct MIDI channels for the MIDI input paths for your MIDI keyboard(s)?
Basically, you define your MIDI ports/channels on the 'General settings | MIDI input paths' screen and then assign those paths (ports/channels) to keyboards and switches (stops etc.) using the 'General settings | Keyboard MIDI inputs' and 'General settings | Switch (MIDI) inputs' screens respectively.
Also have a look at the 'MIDI input' section in the user guide (starts on page 121) for more details about how Hauptwerk v3's MIDI settings work.
If you want to check what MIDI channels your keyboards are using, you can use Hauptwerk's MIDI logging functionality, covered in the 'Learning the Hauptwerk MIDI logging utility' tutorial here:
http://www.hauptwerk.com/support/tutorials/
Also, which edition of Hauptwerk are you using? If the Advanced Edition, do you have any MIDI leads (real or virtual) connected from MIDI OUT ports?