Unless it's explicitly blocked by a firewall rule, the router should pass the traffic -- an IP packet is an IP packet, whatever the contents. (Protocol 41 is IPv6 encapsulated within IPv4). The router itself doesn't need to know anything about IPv6.
Now, if you're using NAT, that will be a problem -- most NAT implementations won't automatically forward protocol 41 packets, and it can be tricky to configure manual forwarding for anything other than TCP or UDP. Additionally, it advertises itself as a 'VPN router'; if your traffic is going over a VPN, it's conceivable that firewall or forwarding rules at one end or the other may be dropping protocol 41 traffic.
To troubleshoot, I'd try simplifying the configuration as much as possible, then adding complexity back in. Start with the box configured as a simple router -- no VPN, no NAT, no firewall rules, and see if it works. Then add the rest of your configuration back in bit by bit, and see what breaks it. Once you know that, it should either suggest a solution, or give you enough information to ask a question with a less vague response *grin*.
First and foremost, there is nothing to fear from being on a public IP allocation, so long as your security devices are configured right.
What should I be replacing NAT with, if we don't have physically separate networks?
The same thing we've been physically separating them with since the 1980's, routers and firewalls. The one big security gain you get with NAT is that it forces you into a default-deny configuration. In order to get any service through it, you have to explicitly punch holes. The fancier devices even allow you to apply IP-based ACLs to those holes, just like a firewall. Probably because they have 'Firewall' on the box, actually.
A correctly configured firewall provides exactly the same service as a NAT gateway. NAT gateways are frequently used because they're easier to get into a secure config than most firewalls.
I hear that IPv6 and IPSEC are supposed to make all this secure somehow, but without physically separated networks that make these devices invisible to the Internet, I really can't see how.
This is a misconception. I work for a University that has a /16 IPv4 allocation, and the vast, vast majority of our IP address consumption is on that public allocation. Certainly all of our end-user workstations and printers. Our RFC1918 consumption is limited to network devices and certain specific servers where such addresses are required. I would not be surprised if you just shivered just now, because I certainly did when I showed up on my first day and saw the post-it on my monitor with my IP address.
And yet, we survive. Why? Because we have an exterior firewall configured for default-deny with limited ICMP throughput. Just because 140.160.123.45 is theoretically routeable, does not mean you can get there from wherever you are on the public internet. This is what firewalls were designed to do.
Given the right router configs, and different subnets in our allocation can be completely unreachable from each other. You do can do this in router tables or firewalls. This is a separate network and has satisfied our security auditors in the past.
There's no way in hell I'll put our billing database (With lots of credit card information!) on the internet for everyone to see.
Our billing database is on a public IPv4 address, and has been for its entire existence, but we have proof you can't get there from here. Just because an address is on the public v4 routeable list does not mean it is guaranteed to be delivered. The two firewalls between the evils of the Internet and the actual database ports filter out the evil. Even from my desk, behind the first firewall, I can't get to that database.
Credit-card information is one special case. That's subject to the PCI-DSS standards, and the standards state directly that servers that contain such data have to be behind a NAT gateway1. Ours are, and these three servers represent our total server usage of RFC1918 addresses. It doesn't add any security, just a layer of complexity, but we need to get that checkbox checked for audits.
The original "IPv6 makes NAT a thing of the past" idea was put forward before the Internet boom really hit full mainstream. In 1995 NAT was a workaround for getting around a small IP allocation. In 2005 it was enshrined in many Security Best Practices document, and at least one major standard (PCI-DSS to be specific). The only concrete benefit NAT gives is that an external entity performing recon on the network doesn't know what the IP landscape looks like behind the NAT device (though thanks to RFC1918 they have a good guess), and on NAT-free IPv4 (such as my work) that isn't the case. It's a small step in defense-in-depth, not a big one.
The replacement for RFC1918 addresses are what are called Unique Local Addresses. Like RFC1918, they don't route unless peers specifically agree to let them route. Unlike RFC1918, they are (probably) globally unique. IPv6 address translators that translate a ULA to a Global IP do exist in the higher range perimeter gear, definitely not in the SOHO gear yet.
You can survive just fine with a public IP address. Just keep in mind that 'public' does not guarantee 'reachable', and you'll be fine.
2017 update
In the past few months, Amazon aws has been adding IPv6 support. It has just been added to their amazon-vpc offering, and their implementation gives some clues as to how large scale deployments are expected to be done.
- You are given a /56 allocation (256 subnets).
- The allocation is a fully routeable subnet.
- You are expected to set your firewall-rules (security-groups) appropriately restrictive.
- There is no NAT, it's not even offered, so all outbound traffic will come from the actual IP address of the instance.
To add one of the security benefits of NAT back in, they are now offering an Egress-only Internet Gateway. This offers one NAT-like benefit:
- Subnets behind it can't be directly accessed from the internet.
Which provides a layer of defense-in-depth, in case a misconfigred firewall rule accidentally allows inbound traffic.
This offering does not translate the internal address into a single address the way NAT does. Outbound traffic will still have the source IP of the instance that opened the connection. Firewall operators looking to whitelist resources in the VPC will be better off whitelisting netblocks, rather than specific IP addresses.
Routeable does not always mean reachable.
1: The PCI-DSS standards changed in October 2010, the statement mandating RFC1918 addresses was removed, and 'network isolation' replaced it.
Best Answer
OK, so you have a number of old IPv4-only devices in your network. Ideally you'd like to be able to continue using them on your IPv6 network, though it seems that you think you can't do so since, well, they're IPv4-only. So now you're looking for other solutions.
Of course, you could replace the offending devices, but the boss won't give you that kind of money!
Enter NAT64.
NAT64 is a router protocol which permits IPv4-only hosts to be accessed from IPv6 hosts. The device implementing NAT64 translates the IPv6 addresses to IPv4 addresses and passes them on to the (hopefully very isolated) IPv4-only network, and translates the other way going back.
There are several Linux and BSD software implementations of NAT64. Microsoft Forefront Unified Access Gateway, as well as some recent Cisco and Juniper routers also implement it.
So, using NAT64, you can isolate and access your IPv4-only devices from IPv6-only hosts. Currently this is the preferred method of dealing with such old hardware.