It seems as if Putty stores the SshHostKeys (and all other configuration) per default in the directories structure where the executable resides. For Silk Performance Explorer this means it's in a temporary folder, e.g.: C:\Users\ youruser \AppData\Roaming\PerfExp\797621411\ where this configuration does not exist yet. And with each start of Silk Performance Explorer you get a new folder, e.g.: C:\Users\ youruser \AppData\Roaming\PerfExp\632565552\... As a workaround create an environment variable ExtraPuTTY_MODE and set its value to REG_MODE . See also http://www.extraputty.com/features/storage.html That means you only need to conform it once and it stores the value here: HKEY_CURRENT_USER\Software\SimonTatham\PuTTY\SshHostKeys
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