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On Windows, both PuTTY and Pageant had a bug relating to Windows data
streams accessed via HANDLE objects (that is, named pipes
or serial ports, rather than network connections). When such a data
stream was closed from the other end, PuTTY would keep a stale copy of
the HANDLE, and close it later, which might accidentally
close some unrelated data stream.
This could affect any usage pattern that involved forwarding Pageant to an SSH server running many subsidiary SSH connections, especially if they ran concurrently. Several users doing that kind of thing reported that PuTTY had locked up and was not responding to any of its agent connections any more.
The bug affects library code shared between PuTTY and Pageant. So it's not enough to upgrade to a version of PuTTY itself without the fix: if you don't also upgrade to a fixed Pageant, you can find that Pageant itself locks up in the same way, with the same user-visible effect.
However, as of dde659004083b575547f2740aaa56fdf64523770, we believe this issue is fully fixed. Nobody has reported it occurring when both the PuTTY and Pageant in use contain that fix.