Due to a known issue with the Quartus® II software versions 11.0 SP1 and earlier, the PC version of the tools does not allow STDIN inputs to be obtained from the System Console gui window. This issue does not affect the Linux version of the tool.
To work around this issue, it is possible to open System Console in an interactive command line mode, using the following commands:
cd %QUARTUS_ROOTDIR%\sopc_builder\bin
system-console -cli
This issue is scheduled to be fixed in a future version of the Quartus II software.