Hi Andre,
The issue we experienced was with the SAP Password manager (used for non SAP systems), even after SAP fixed a bug we found the user experience very poor and decided that this aspect of the product was not fit for purpose.
Your challenge sounds more like the SSO component for SAP applications, we never faced any major issues with this part (we use for CRM web UI also), but there are various logging options available to help track issues. Its worth checking you are on the latest SSO 2.0 patch level at client/server and if the problem persists then ask you basis team who may need to raise with SAP.