The resolution is to upgrade to Cloud Access Manager 188.8.131.5210 HF4.
After applying the Hotfix it is necessary to manually update all applications that use Primary credentials.
For each application affected:
1. open the Application Name tab in the Edit wizard
2. Uncheck the "Use primary credentials..." checkbox
3. Save the application
4. Return to the Application Name tab in the Edit wizard
5. Re-select the "Use primary credentials..." checkbox
6. Save the Application again
This will reset the applications to use the correct credential set for the STS.