We have a portal running in Sandbox, Development, and QA landscapes. (We haven't implemented production yet.) We have SSO configured in the Sandbox and Development environments. While configuring the QA portal we discovered this problem.
Using Internet Explorer, I browsed to the development portal and SSO to one of our SAP systems with no issues. I then browsed to the QA portal to review some configuration. So at this point I have IE 7.0 with 2 tabs open - one with the Development portal and one with the QA portal. When I changed back to the development portal and click on a link to SSO into an SAP system it failed with an error indicating the system alias wasn't set up. I also noticed when I browsed to a custom WebDynPro application on the development portal it didn't want to load with permissions problems.
I closed out Internet Explorer and loaded the development portal up again and everything worked just fine. I closed out of IE and loaded just the QA portal and got the errors above but was expecting these errors while we were configuring it.
So, just to test I closed IE and reopened. I first browsed to the QA portal and got the same errors I was expecting. I then browsed to the DEV portal and was able to SSO into our SAP systems and use the WebDynPro application without errors.
It seems the portals are "sharing" something (a cookie?) that causes them to cross-pollinate when javascript is used. Whichever portal is the last to be loaded apparently takes precedence. Any ideas on how to configure the portals so this doesn't happen?