We are running Exchange 2013 on a Windows 2008 R2 Enterprise box. It had cumulative update 1 installed, and the security update. I first went to install cumulative update 2, but was met with an error that I needed to remove the security update.
When I went back in to remove the security update, all the Exchange services had been disabled, so the uninstall simply flashed up then disappeared and remained under “View Installed Updates”
I had to re-enable all the Exchange services manually, start them, the re-run the installer. This time it was successful.
I began the Cumulative Update 2 setup.exe file again, and this time it began to do the update. It failed at step 5 of 11, citing an iisreset error. I then tried running setup.exe with the appropriate switches from the command line, to avoid any issues with elevating to administrative permission. Failed at the same place.
I finally found this Hotfix on Microsoft’s website: http://support.microsoft.com/kb/975443/en-us
After removing some pending file rename operations so that I could skip a reboot, I installed this, then re-ran the setup for CU2 via command line. It completed successfully.