I can't explain this, but when I checked today, I was able to access the problem computer through the VPN without issue.
I was investigating the IP tables you flagged as being potential problems, and traced two of them to a VPN policy routing package I'm using. Disabling this removed the tables 102 and 103 from the output of ip -4 ru, and when I checked, access over the VPN was possible. I re-enabled the package and rebooted, and access is still possible. However, I didn't try accessing the problem computer immediately before disabling the package, so I can't be sure if it had an effect or not.
The only thing I haven't done yet that might break things again is reboot the problem computer. I'll try this and see how it goes over a few days and report back. Fingers crossed...