O Ubuntu 11.10 contém uma versão mais recente do PuTTY ( 0,61 ) vs. Natty (0.60 ).
Algo poderia ter sido quebrado na atualização. Aqui está um changelog relevante ( Fonte ):
These features are new in beta 0.61 (released 2011-07-12):
Kerberos/GSSAPI authentication in SSH-2.
Local X11 authorisation support on Windows. (Unix already had it, of course.)
Support for non-fixed-width fonts on Windows.
GTK 2 support on Unix.
Specifying the logical host name independently of the physical network address to connect to.
Crypto and flow control optimisations.
Support for the [email protected] SSH-2 compression method.
Support for new Windows 7 UI features: Aero resizing and jump lists.
Support for OpenSSH AES-encrypted private key files in PuTTYgen.
Bug fix: handles OpenSSH private keys with primes in either order.
Bug fix: corruption of port forwarding is fixed (we think).
Bug fix: various crashes and hangs when exiting on failure.
Bug fix: hang in the serial back end on Windows.
Bug fix: Windows clipboard is now read asynchronously, in case of deadlock due to the clipboard owner being at the far end of the same PuTTY's network connection (either via X forwarding or via tunnelled rdesktop).
Você pode investigar mais sobre a página lista de desejos do PuTTY.