I was facing the exact same issue running Gnome Shell 3.12 on ArchLinux x86_64 with an Intel HD 4000 and it looks like I just found a solution (well, at least for me).
Basically all I did was adding the TearFree option to my /etc/X11/xorg.conf.d/20-intel.conf. I had it already created earlier in order to enable SNA acceleration, which I then disabled again due to a lack of any noticeable performance improvement.
Anyhow, this is what it looks like:
Identifier "Intel Graphics"
# Option "AccelMethod" "sna"
Option "TearFree" "true"
And Bam! - smooth sailing from here on.
I stumbled upon this more or less completely by accident, so I'm not really sure whether this a fix or rather a dirty hack, but like I said, it did the trick for me quite nicely.
So from all I can tell, this seems to be an framerate/vsync related issue (with Mutter running on 60 fps via default)?