I would suspect two possible issues.
a. Have you engaged operated the inter manual couplers of the St Anne Organ somehow? (See the description in the HW manual of a typical pipe organ if you don't understand this..)
or
b. The midi data coming from the Nord is not separated into distinct midi channels. By default the Nord sends midi data out on separate changes. It says in the Nord manual (pg 20)
how to change the midi channels from the System Menu but the defaults should be fine....
"MIDI Upper Channel
This sets the MIDI Channel that the upper/swell manual on the Nord
C2D transmits and responds to.
Range: Off, 1-16 (default = 1)
MIDI Lower Channel
This sets the MIDI channel that the lower/great manual on the Nord
C2D transmits and responds to.
Range: Off, 1-16, (default = 2)
MIDI Pedal Channel
This sets the MIDI channel that the Bass section of the Nord C2D
organ transmits (if the Great manual is split) and responds to.
Range: Off, 1-16, (default = 3)
If the midi channels for each manual and pedal board and the x-keys are different from each other, when you auto detect each manual then HW should only use only key presses from that manual to play that division of the organ.
I would try to solve the issue by having only the Nord system connected to the computer system.
1. I would reset the Nord to its default settings (if this is not too disruptive to your other use of the Nord).
2. I would set the Nord Midi local control (pg 20) to OFF so that the Nord would not sound its native voices.
3. I would use a program like midimedic (rather than Hauptwerk itself) to check that each manual and the pedal board were sending data on a distinct midi channel. (Load midimedic and not Hauptwerk...)
http://www.midiworks.ca/index.php/37-downloads/downloads/11-midi-medic-1394. Once each keyboard and the pedalboard were transmitting on separate channels, I would close midimedic and load Hauptwerk.
5. I would make sure that the midi input from the Nord was the only console midi input enabled in HW.
6. I would reset the midi settings for the St Anne virtual organ.
7. I would then auto detect the Swell division (top manual).
8. I would check it worked by drawing one swell stop and seeing that it played only from the top manual.
9. I would check that this sounded like only one stop! If it sounded like more I would check that the St Anne organ's full organ or crescendo pedal were not active.
10.If it played from the other manual or pedals I would check if the Swell to Grt (Swell to Pedal) were active and it they were clear them.
11. I would repeat steps 7-10 for the Great and Pedal organ
12. I would auto detect the swell pedal
Then and only then I would try to use the X-keys. These would need to be ona separate midi channel from any midi input coming from the Nord.
Good luck.
Iain