Well, there's a couple more steps in here than just loading the code.
In short, you must use the cRIO reimaging utility to install the BlackJaguarPlugin in the cRIO.
Also, the Jaguars must have updated firmware. (Done through the BDC-COMM)
The other things you must watch out for is that the code is made to work with Jaguars at certain Device Numbers.
I apologize about the lack of documentation in my code. I'll try to have a more complete package uploaded soon.
EDIT:
Here's a more complete package:
http://kamocat.com/robot/electrical/CAN_resources.zip
It will fail out-of-the-box if you do not have encoders attached, or if the Jaguars do not have the correct device IDs. However, both of these things can be changed in Begin.vi
Fritzdejongh, your best option would be to meet with a local team and have them test your hardware with their functional equipment. Something is obviously different between your BDC-COMM setup and your cRIO setup. It could be as simple as a poor connection (bad connection within the cable caused by stress from bending, dirty contacts on your cRIO RS232 port, a poorly seated connector), or something as bad as an issue in your cRIO firmware or your LabVIEW install. It could even be interference (from the netconsole trying to use the cRIO's RS232 port, or from electrical noise around the cable).
Again, your best option is meeting with someone who has CAN working over the RS232. I can't help you much without being there with your robot.