@Sn3ak:
I too had this problem, however I saw another post, and found clicking save on the He.net interface, fixed the issue, however on reboot it came back.
My solution to the problem, was to change the recommended /128 subnet on both sides of the tunnel and made it a /64 as He.net specifies.
Multiple reboots later, it's still coming up automagically and working.
Hope this helps..
Mine survived a reboot, and then the update to the next nightly just fine once I "edited and saved" the gateway again, although I've always been using the /64 CIDR.
Did you always have the issue with the route dropping? Or was it after a certain update?