Yes, it definitely helped. Thanks for reporting the problem so specifically.
Please give version 2.19 a try, now on the beta page:
http://www.topofusion.com/beta.phpI'm not sure if I have nailed the tracklog downloading inconsistency, but I am fairly sure I fixed the waypoint problem you're having. I was able to duplicate it on my 60CS. It would always get an error on a certain waypoint.
The track downloading, unfortunately, is very hard to test since it almost always works for me.