Slacker,
Thanks for your reply.
I typed your suggested nios2-elf-gcc command and received the output in the gccNiosConfig.txt file.
Some of the output does look odd, like all the nonexistent directories. For comparison purposes I ran the same command on a different PC which still has the 7.2 version of the Altera tool set installed (gccNios72Config.txt). The output looks similar to the 9.0 installation I have, which leads me to believe that the uninstall of 7.2 and install of 9.0 didn't create the problems I am having.
The command actually hangs after you see "End of search list." so this didn't seem normal either. Ctrl-C gets you back to Cygwin...
I looked into some of the directories listed at the end, and I don't find stdio.h, but I do find stddef.h in "/cygdrive/c/altera/90/nios2eds/bin/nios2-gnutools/H-i686-pc-cygwin/lib/gcc/nios2-elf/3.4.6/include". I'll try adding this to my RTRT build.
I will also look into the software build tools option as you suggested.
Cheers
Tim