The SIMD8 GS backend doesn't implement support for instanced geometry shaders yet. This should be relatively simple.
Notably, the thread payload is different when InstanceCount > 1 - the ICP handles are layed out differently. There may be a few other differences too.
Unfortunately, it appears that we have no Piglit tests that verify that instanced GS inputs work properly. All instanced GS tests pass today with the assert removed, when there is obvious code missing.
I added this support in Mesa 12.0 apparently. I also wrote a Piglit test in commit 41fee6eba3537361dbf3bca73f0f2c6756c57c39.