When running an upgrade on the FIM Service and Portal the upgrade rolls back without warning or error. 

A verbose log of the installed captures more details:

Action 15:31:56: GetCertThumbprintFromName.

MSI (s) (A4:2C) [15:31:56:368]: Executing op: CustomActionSchedule(Action=GetCertThumbprintFromName,ActionType=11265,Source=BinaryData,Target=**********,)

MSI (s) (A4:B0) [15:31:56:381]: Invoking remote custom action. DLL: C:\Windows\Installer\MSI77FC.tmp, Entrypoint: GetCertThumbprintFromName

MSI (s) (A4:58) [15:31:56:381]: Generating random cookie.

MSI (s) (A4:58) [15:31:56:383]: Created Custom Action Server with PID 4756 (0x1294).

MSI (s) (A4:3C) [15:31:56:398]: Running as a service.

MSI (s) (A4:3C) [15:31:56:399]: Hello, I'm your 64bit Elevated custom action server.

CustomAction GetCertThumbprintFromName returned actual error code 1603 (note this may not be 100% accurate if translation happened inside sandbox)

Action ended 15:31:56: InstallExecute. Return value 3.


 Unknown.  Issues seems to come up with upgrade from 4.0.2592


 Prior to attempting the upgrade again, run a change-install on the FIM Service.  Be sure to generate a new certificate during the install.  Once the change-install is completed, perform the upgrade on the FIM Service and Portal.