Strange it should look for it in /usr/include thats where the file should be.
What I notice is that if you use cflags you can get problems.
Unset them with the following command.
export CFLAGS="-O2 -march=i686" &&
and rebuild zlib and then retry file again.
Hope it works for you then...
Zlib is known to build its shared library incorrectly if CFLAGS is specified in the environment. If using a specified CFLAGS variable, be sure to add the -fPIC directive to the CFLAGS variable for the duration of the configure command below, then remove it afterwards.