You may see these error messages when executing certain Nios® II makefiles or Cygwin executables on systems using Windows® 7. This is due to the way the Quartus® II software toolset is handling the changes in the security model in Windows 7 which was significantly changed from that of Windows XP. Because of this, Quartus II software version 10.x and 11.0, produced these errors.
The makefiles that include the keyword "update" in the file name are susceptable to this issue, i.e. nios2-app-update-makefile.exe, nios2-lib-update-makefile.exe, nios2-bsp-update-settings.exe. In addition, all the executables in Cygwin, such as patch.exe are susceptible to this issue.
This issue has been fixed in Quartus II software version 12.1 SP1 and later.
If you cannot upgrade to this version, try disabling User Account Control, UAC, in the Control Panel, User Accounts setting.