@Zester, It took me a while to figure it out, but tweaking the default UV window of blender will cause the "something went wrong" problem. if you don't tweak the window, it works fine on 2.65a (so just create another layout if you need uv mapping and it's alright)
@Anael, Giles gives great results however it is ALOT of extra work (importing/exporting/managing textures names, re-assigning everything, etc), and render time (even preview renders) are quite long also.
Well, that's still an alternative for those who can't stand blender
But now honestly with the Atlas plugin there's no reason to look somewhere else, lately i've done alot of tests with Texture Atlas plugin and yeah, it's just awesome.
There's only one thing that kill your workflow : Texture paths (for spec and normal maps), i definitely can't find a good way to organize everything in a manner that you don't have to edit anything