I still have this problem with Mesa 9.2-devel (git-4deefd9)
( patched with:
 r600g: emit a ps partial flush after CP DMA
 r600g: enable CP DMA on r6xx (v3) )
The night times scenes work better with force_glsl_extensions_warn=true

I saw this problem with Unigine Heaven 3.0, Heroes of Newerth 3.0.3 (also 2.x)
and Xonotic 0.6.0 .

I think the last one is interesting because it is under GPL and works fine if I
just enable shadows from realtime world lights but shows the problem if I
enable "Soft shadows" too. The tooltip of "Soft shadows" is:
[enables use of shadowmapping (depth texture sampling) instead of stencil
shadow volumes, requires gl_fbo 1]
The problem in Xonotic can be seen only in a few places with dynamic world
lightning, like some rooms with lava in level 6 and the lights behind some big
fans in level 8.

HD3850 (RV670) AGP, kernel 3.8.0