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We've had some reports of crashes when moderately large clipboard operations are performed. Typically this is associated with use of the "Copy All to Clipboard" menu action, but it can happen with ordinary mouse-button copy-and-paste too.
It turns out that PuTTY can crash when attempting to copy a large (> 5 kilobyte) chunk of text containing a significant number of consecutive empty lines. (More than 100 after the 5k mark would likely guarantee a crash or other misbehaviour, but it could happen with fewer.)
Audit trail for this bug.