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We've had a report that PuTTY's IPv6 support doesn't work in Windows Vista (x86 RTM version from MSDN), and it always falls back to IPv4:
As far as I can see, connections via IPv4 work exactly as they should. With IPv6, however, it would appear that regardless of the mode I specify (either Auto or IPv6 on the Connection section of the configuration, that PuTTY always connects to the relevant IPv4 socket at the remote end, and never the IPv6 socket. This is also repeatable using the command line: i.e.
putty -6 -ssh my.host.namealso connects via IPv4.
It is also not possible, using Vista, to connect to an IPv6 address literal either via the PuTTY user interface itself or the command line. In my case I was trying to connect to my server 2001:8b0:127::2 but this was refused with the error message 'Unable to open connection to server 2001:8b0:127::2 gethostbyname: unknown error'
(I understand that Microsoft have changed the Winsock interface in Vista so this may have some bearing on the problem.)
SGT, 2006-12-24: Jeroen Massar, the original author of PuTTY's IPv6 code, has supplied a patch which fixes this. Users experiencing this bug might like to download a post-r7007 snapshot and make sure the problem has gone away.
Audit trail for this bug.