Sorry for the delay guys, I ended up working late last night. Thanks for that suggestion qas, I hadn't thought of that (d'oh)... In modem mode my Debian desktop (Intel Pro 1000MT NIC, cat6 cable) gets 15MB/sec from an Ubuntu torrent. Add in the VPN (no SOCKS5 proxy), and I still get 15MB/sec.
Once back in router mode, I can't get full speed from the VPN unless I use a SOCKS5 proxy as well. So it's definitely an issue with routing/handling on the SH2. Quel surprise! The wifi is definitely better on SH2 so I'll just keep that running and use the SOCKS5 dirty fix for now to keep full speed on downloads and uploads (I'm a Linux tester/dev so I distro-hop and circulate patches etc almost continuously).
Is there an email I can report this issue to VM, so that they can look to adding a fix to a future firmware update? Or should I just not hold my breath? Again thanks to all replying to this thread, at least now I've confirmed the issue and have a temporary dirty fix.