Crap, that was a debugging thing I did - I'll have that fixed in the next commit. I removed the time restriction so I can see all the flights, since I wasn't flying at the time.
I think nav points problem might have to do with the way I'm calculating distance, so I'm working on that.
http://dev.phpvms.net/routetest.php?depicao=SAWH&arricao=SBGR&route=GRA+UT101+MDP+UA310+CRR+UM540+POR+UA314+FLN+UW21+ANISE&submit=View+Route
But in the case of JUICE, the coordinate which is further is actually the correct one, so I'm trying to find out what the proper way of calculating is.