I have encountered the same and I have got the reply from Altera. I re-installed my systems and they are working now.
The repy information are as follows:
I believe you need to do a reinstallation of Altera's software. Please be noted with the following consideration during your reinstallation:
1. Please make sure you only have Quartus II 6.0 and Nios II 6.0 installed. You can not have multiple versions installed since this will cause SOPC Builder components to mix and not operate correctly.
2. Make sure that you do not have any other versions of Cygwin installed on your PC. If you have, please remove it first.
3. Try uninstalling all Altera software, re-install QuartusII 6.0 first and then Nios II 6.0.
4. Run SOPC builder once after installing NiosII, as SOPC builder sets up a few PATHs and updates some of the files needed by the NiosII IDE. Launching the SOPC builder within a standard reference design should ensure all the paths are setup, then relaunch the NiosII IDE.