Hmm... sounds like the Make process couldn't find the autoconf file that's generated during the building of a linux kernel.
Things to confirm:
- Double check the Linux Build Location option in the uClibc menuconfig. It should point to a kernel project build directory,
not to the linux source tree.
- The kernel project that's specified within the uClibc menuconfig must be built at least once to generate the autoconf.h file
- After building the kernel, does an autoconf.h file exist inside the build directory? I think it should be in
<kernel_project>/build/include/linux
Hope that helps, if not let me know and I'll dig a bit deeper.