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In 0.58, a new SSH bug-compatibility mode was added to PuTTY: "Handles SSH-2 key re-exchange badly".
However, in 0.58, attempts to save any setting other than "Auto" fail - the setting stays at "Auto". (Apparently there is some NetApp server - "Data ONTAP" - that needs this mode and can't be distinguished by our heuristics.) This is fixed in the development snapshots.
If the setting is present in the saved settings, 0.58 will happily load it, so a workaround for 0.58 users is to use a snapshot just to save the setting to the desired value, and then revert to using 0.58. (Alternatively, you could edit the setting manually; its name is BugRekey2 with values 0=Auto, 1=Off, 2=On.)
Audit trail for this bug.