soz to keep picking on old topics that peepz have probz already sorted out but incase u havent...
load ur map and open the console. Type : "Nav" and a list of different nav commands come up (that ur probably already aware of) u can set different navigation types wherever ur standing, stick the appropriate ones where u want them then generate ur navigation mesh again, shud work. If it doesn't then i'm talkin complete testicles and should spend more time proving it before attemptin 2 help :
hmm.. bitching about myself?? wait..thats ur job