Komodo saves all of it's settings in it's profile folder, if you want to start Komodo with the default settings there's 2 things you could do:
When Komodo looks for the profile folder and cannot find it it will create a new profile folder with the default settings.
Before following these steps please ensure that Komodo is not running.
You can set the location where Komodo looks for its profile folder with the KOMODO_USERDATADIR environment variable. It's value should be set to the parent folder that you wish for Komodo to look in.
"C:\Program Files (x86)\ActiveState Komodo IDE 9\komodo.exe"
Please see the Reset Komodo Documentation.