I've got two tunnels, one on each WAN. Both are online, and thanks to NPt and some gateway groups, I have working IPv6 multi-wan. Not sure why others might be having issues, but the same things apply as usual.
1. Make sure you have a distinct tunnel endpoint for each tunnel. For example, one to Chicago, one to Dallas, one to NY, etc. Don't use the same HE.net endpoint for more than one.
2. Make sure all your WANs allow ICMP from the endpoints
3. Perhaps add a static route to the remote endpoint node to make sure they use the proper WAN