Due to differences between ConfigMgr 2012 RTW and SP1 the same PCM code base needed to be compiled differently for these versions. This means that the installer needed to determine which set of binaries to install on a machine based on the Configuration Manager console version. To determine this the installer looks at the version of Microsoft.ConfigurationManagement.exe and then installs the appropriate set of binaries. The installer is looking in the default location, %programfiles(x86)%\Microsoft Configuration Manager\AdminConsole\bin, for this binary and if it doesn't find it the installer still appears to install successfully. However, PCM wasn't actually installed at all.
Before I get into the actual workaround let me just say there have been a few people who I talked to about the problem and they all asked, "Do I really need to uninstall my console and reinstall it to the default location?" No, you do not need to reinstall your console to the default location. Yes, that will work, but we should be able to get it to work without reinstalling the console at all. Currently the best workaround to get the appropriate set of PCM binaries installed is to copy the Microsoft.ConfigurationManagement.exe from wherever the console is currently installed into %programfiles(x86)%\Microsoft Configuration Manager\AdminConsole\bin (creating the directories if you have to) then run the installer.
We are still checking into our options, but in the meantime I hope this helps those of you that are running into this issue.