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If you're cross compiling you absolutely don't want to use your natively compiled boost directories - i.e. do not use /usr!
You need to look for where your cross compiled boost libs are actually installed - usually this will be inside your toolchain. I notice from the wiki page you link to the instructions:
cp -r $CTC_USR_DIR/lib/libboost* $TARGETDIR/libs/
The short of it - $TARGETDIR/libs should be what he's attaching to LD_LIBRARY_PATH in setup.sh to find boosts's libs. Just make sure it's empty to begin with (notice the export LD_LIBRARY_PATH= # just to be sure just above) otherwise it will pick up your native libs.
Is there another variable you are trying to set to help with boost?
Actually, hacking it this way is a bit ugly - cmake would be much better here.
For more details:
If you want to be absolutely sure you have the libs, have a look in $TARGETDIR/libs/. You should see libboost*.so in there. You can actually check that they're cross compiled by running file on the command - e.g. in my arm toolchain:
file libexpat.so.0.1.0
libexpat.so.0.1.0: ELF 32-bit LSB shared object, ARM, version 1 (SYSV), dynamically linked, not stripped
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