There is two major places to change the search directories.
The compiler settings and the project/task settings.
You likely have only fixed one of them.
NOTE: I had to add the Cygwin include folder to search list for rpc.h to be found.
You will need to change "C:\GreenApps\Cygwin1_7" to "C:\cygwin"
I added include search folder "C:\GreenApps\Cygwin1_7\usr\include\tirpc"
Edit: This might work also "$(TARGET_COMPILER_DIR)\usr\include\tirpc".
My build command. Updated because I saw two search folders removed one.
i686-pc-cygwin-gcc-4.exe -Wall -g -IC:/GreenApps/Cygwin1_7/usr/include/tirpc -c H:/SourceCode/Projects/test-i686-w64/main.c -o obj/Debug/main.o
i686-pc-cygwin-g++-4.exe -o bin/Debug/test-i686-w64.exe obj/Debug/main.o -ltirpc
Note: "H:/SourceCode/Projects/test-i686-w64" is my project folder.
Tim S.