Finally after nearly 12 months of on and off fiddling - I'm able to run boinc as a daemon/service and have it recognise the gpu.

http://forums.gentoo.org/viewtopic-p-6549319.html#6549319

Step 1 - emerge ati code with OpenCL support
Edit /etc/make.conf

VIDEO_CARDS="fglrx"

Add OpenCL support

echo "x11-drivers/ati-drivers opencl" >> /etc/portage/package.use
echo "dev-util/opencl-headers" >> /etc/portage/package.keyword

Re-emerge all packages with new USE flags

emerge -avDN world

Step 2 - Set OpenGL to ATI

# eselect opengl set ati

Step 3 - Configure X for fglrx

# aticonfig --initial
# aticonfig --initial=check

Step 4 - Add OpenCL symlinks

ln -s /usr/lib32/libOpenCL.so.1 /usr/lib32/libOpenCL.so 
ln -s /usr/lib64/libOpenCL.so.1 /usr/lib64/libOpenCL.so

Step 5 - Create a symlink to libaticalrt.so

ln -snf /usr/lib64/libaticalrt.so /var/lib/boinc/libaticalrt.so

Step 6 - Edit /etc/conf.d/boinc
you want to change the boinc references to your username

# Owner of BOINC process (must be existing)
USER="boinc"
GROUP="boinc"

eg.

USER="trogdog"
GROUP="trogdog"

Step 7 - Edit /etc/init.d/boinc
we want the boinc service to be the last thing that starts

after xdm local

depend() {
# we can use dns and net, but we can also in most cases live without them
use dns net
after xdm local
}

Step 8 - Check that boinc will indeed recognise your gpu

/etc/init.d/boinc start

---

CIC1=CC=C(C2=N[C@@H](CC(OC(C)(C)C)=O)C3=NN=C(C)N3C4=C2C(C)=C(C)S4)C=C1