You may have selected all SAP GUI features, including SNC Client Encryption. This changes the SNC product configuration, i.e. the system environment variable "SNC_LIB".
To check this, open a DOS box and type "set". You should see SNC_LIB=<path-to-dll>. If this is not your SSO solution, either fix the variable manually, or reinstall your SSO client.
Btw. Is it SAP SSO Secure Login Client you are using?
-- Stephan