make install puts files in wrong place?

[Randy Yates]

I'm running configure as follows:

./configure --host=arm-arago-linux-gnueabi
--prefix=/home/embedded-linux/tool/ti-sdk/board-support/linux-nelson-patched-with-bluez-5.2/usr
--sysconfdir=/home/embedded-linux/tool/ti-sdk/rootfs-partial/rootfs-partial/etc
--with-sysroot=/home/embedded-linux/tool/ti-sdk/board-support/linux-nelson-patched-with-bluez-5.2
--localstatedir=/var 

However, when I make install, it is placing the include files into 

/home/embedded-linux/tool/ti-sdk/board-support/linux-nelson-patched-with-bluez-5.2/usr/lib/libffi-3.0.11/include/ffi.h

I would've expected them to be placed somewhere under 

/home/embedded-linux/tool/ti-sdk/board-support/linux-nelson-patched-with-bluez-5.2/usr/include

Am I doing something wrong or is this a bug in the configure?
-- 
Randy Yates
Digital Signal Labs
http://www.digitalsignallabs.com