Even when running at a constant 60fps, indoors (buildings and dungeons) the stuttering is very noticeable. However if I run the game in windowed mode (keeping all the other settings unchanged) the problem disappears and the difference in the smoothness is staggering.

This happens with both 1.3.10 and 1.4 beta. Unfortunately multi GPU is not supported in windowed mode for DX9 games so I am forced to choose between smooth gameplay outdoors vs smooth gameplay indoors

For the record this is my PC:
Asus P8Z68-V Pro
i7 2600k@4.4Ghz
16GB DDR3 1600
2x 6970 2GB
Win 7 x64

fps limiter = your friend

Try 59 or 60 to start. For me, it doesn't go away completely until I tweak my monitor refresh to 64 and set the limiter to 64. But each computer is different.

I have same mobo, cpu, RAM and OS as you do.

You have a few options on how to do this:
DXtory - although people reporting this isn't working with 1.4 beta
nVidia Inspector - latest version has built in limiter option, pick you number (you can customize to by editing config file if the number you want isn't on list)
ENB - the enb shader has a limiter option within its ini.

For me, I find the ENB the most effective and convenient, but they all do the same thing.

Thanks for the reply and suggestions. I tried DXtory and it kinda works: indoors stuttering and lag is much better (not as smooth as windowed mode), but the problem is that it also killed my fps outdoors by 10-15. Where I was getting 60 now I get 45-50). I tried another fps limiter mod, but the screen tearing caused, is even more annoying than the microstuttering. Can you give me the exact link for the ENB mod (I came across several variations and I am a bit confused).

/rant on
I still can't believe that the 64hz bug is still around since Oblivion and it managed to get "ported" to all Bethesda games ever since and most likely will not get fixed in Skyrim either.
/rant off

http://www.skyrimnexus.com/downloads/file.php?id=822 is my favourite, but ENB does much more than have a limiter function, and it comes at a major performance cost. Btw...tearing? Have you turned iPresentInterval ie vsync off?

Ya...the 64hz bug...I'm embarrassed for Bethesda on that one.

I'll give that a try, thanks. Yes the the http://www.skyrimnexus.com/downloads/file.php?id=34 I tried would fix the stuttering but forced vsync off without any way to enable it back on.

One solution is to download an "antilag" file with a d3d9.dll but this caused some really bad screen tearing. The other, which I was using up until recently, was to run in windowed mode (but as you said, disables crossfire). There are a few other solutions that either don't work or have other weird side effects.

The fix that worked for me was capping the FPS to 59, and v-sync still works (so no screen tearing). In the latest beta of http://forums.guru3d.com/showthread.php?t=357421 they added framerate capping (Nvidia recently added this into their drivers I believe... come on AMD!). Just add TESV.exe to the application profile properties, click the setup icon and add 59 into the framerate limit box. I can finally play the game with crossfire, in fullscreen mode and without the mouse skipping/stutter. Message me if you need better instructions.

With 1.4 beta, you just need Dxtory open. In the fps limit box put in 60 but do not tick the box. Using the limiter at 59 or 60 with the box ticked causes issues with grids loading, LOD, and sound cutting out (only in 1.4).

That fixes my stutter, but in 1.3 you need to tick that box and set it to 59.

If its dropping your framerate then something else is the problem, because using dxtory in the way I and nanny said is just like a fps display programme like Fraps.

Quick Edit:
Maybe when you're using it you're pressing the hotkey to record gameplay videos by mistake

Thanks. I assumed that if you entered 60 in the frame limiter field, the box has to be ticked in order for the setting to be applied. I will try this evening without ticking the box.

I tested different configurations for a few hours the other night and the one I posted here worked.

Setting the box to 60 without the tick doesn't limit the fps, but for whatever reason for me the configuration I use fixes first person stutter and has no discernible side effects.

Thanks a bunch for the IM communication! That was very nice of you. Unfortunately, it's not working for me. I tried limits of 60 (my monitor is 60Hz), 59, and 30, and none of them stopped the stuttering. I actually got to the point where I was comparing the indoor FPS with two HD 5970s in Crossfire vs. windowed, and my indoor FPS under windowed mode was a constant 60 with no stuttering. With Crossfire, it was 60 until I turned in any direction, at which point it dropped into the low 40s and had tons of stuttering. So, basically, 1 GPU=60 FPS, 4 GPUs=40 FPS. What the heck is that about?