When you install BizTalk 3013R2 CU2, there is an undocumented requirement that you need to have BizTalk already configured.
If you don’t, you will get the following error
And when it finishes
If you look in the event log, you will notice this entry, which lead me to the belief that you need to have configured.
Framework Version: v4.0.30319
Description: The process was terminated due to an unhandled exception.
Exception Info: System.
I configured it, ran it and it worked.
The download page states nothing about BTS needing to be configured, (To apply this cumulative update package, you must have BizTalk Server 2013 installed. ) nor is the Readme.txt available.