yes flow-based IPv6 traffic using an HE tunnel got broken in 10.4R1, yet runs just fine in 10.3R2. Packet-based IPv6 will work in 10.4 with an HE tunnel though. But you get no stateful inspection, etc. There are two threads about this in the SRX forum --
HE IPv6 tunnel in 10.4 not working
10.4 is out - this one has stuff about IPv6 HE tunnel not working later on in the thread.
it's unfortunate since I believe 10.4 added a whole bunch of IPv6 features...I suspect a lot of people using IPv6 today on SRXs are testing it out and putting it through its paces before deployment with HE tunnels, so now they have no way of testing those new IPv6 features.
Maybe 10.4R2 will fix it....
Cheers,
Will