This may be related to the CDROM drive letter changed after Windows 2012 R2 base setup and the moment you OR a third party software tries to install
Framework 3.0/3.5 in the background and does not find the 2012 R2 Media.
Also there are three patches which could disturb the installation
It's unclear if MS fixed those three since the first appearing of the problem
Here is how to uninstall them and after you add 3.5 you can install them again. A lot of products need Framework 3.5 (Exchange 2010, Mcafee EPO 5 and
also WSUS-Windows Update Server, SQL Express 2007/2012). This is the first step you will have to do on those Servers.
Uninstall those three patches:
wusa.exe /uninstall /kb:2966826 /quiet /norestart
wusa.exe /uninstall /kb:2966827 /quiet /norestart
wusa.exe /uninstall /kb:2966828 /quiet /norestart
Reboot the Server
Make Sure the Server 2012R2 CD is in the Drive you specify
(Source:d:\ = CDROM Drive with Server 2012 IS D: )
In this sample Z: is the 2012R2 DVD media
dism /online /enable-feature /featurename:NetFX3 /all /Source:Z:\sources\sxs /LimitAccess