4.2.3 ‘Flush log file frequently’

This option allows you to control how frequently logged data is flushed to disc. By default, PuTTY will flush data as soon as it is displayed, so that if you view the log file while a session is still open, it will be up to date; and if the client system crashes, there's a greater chance that the data will be preserved.

However, this can incur a performance penalty. If PuTTY is running slowly with logging enabled, you could try unchecking this option. Be warned that the log file may not always be up to date as a result (although it will of course be flushed when it is closed, for instance at the end of a session).