I used to use Cygwin, but when I installed Quartus II and Nios, my local installation stopped working; it couldn't find cygwin1.dll. Rather than fight that, I remove my local installation of it, uninstalled Quartus II and Nios II and reinstalled everything. To no avail the binaries under C:\altera\kits\nios2_60\bin\nios2-gnutools\H-i686-pc-cygwin\bin doesn't run.
Incidently, the Nios II Dev Board, reference manual seems out of sync. In "Appendix B: Restoring Factory Configuration, step 1" the directions to launch the SDK Shell doesn't match the menus -- in fact, there aren't any SDK Shell under the Altera menu.
I'd be much obliged for any help here.
Thanks, Tommy