All PuTTY settings are available in registry. The path to have access to keys:
HKEY_USERS\UID\Software\SimonTatham\PuTTY\Sessions\Default%20SettingsThe UID part is unique and will be different on your computer.
My main issue was PuTTY was not able to save the default settings and in particular, my font parameter. So I update them directly in registry:
Be careful when you edit manually those keys, it can lead to some unpredictable behavior if parameters are wrong.
FrenchSavvy 