I have communicated off-line with Anders. As it turns out, the course in question is an MTB-O course.
For an MTB-O course the course length is to be calculated along the best route choice.
Condes supports this. When a course is designated "mtb-o course", then there is a "course length line" that goes from start to finish. The course length is calculated as the length of this line. In order to get the correct course length, you need to manipulate this line (add corner points) so that it follows the best route choice on the course.
There are two alternative options, if you don't want to let the route choice line determine the course length:
1) Designate the course as a "normal course". The course length will then be calculated as the accumulated length of the course legs.
2) Calculate the length manually, and enter the length manually in the course dialog window (first remove the check mark for "Use calculated length")
Best regards,
Finn