I was having this same problem, and found one cause.
I have an extensive library on a Drobo FS. None of the AppleTV's in the house have any problem streaming full 1080p from it, but my new iMac does. Choppy / laggy video play. Movies and TV shows right from the iTunes store. I can have 3 TV's streaming, and even a 4th laptop, all streaming from the iMac iTunes using the Drobo. They all have zero issues. No lag, no choppy, nothing. iMac has the issue even when nothing else is running. Every time.
BTW, it's happend on my old iMac and the brand new one, both with iTunes 11.
I was told to try setting up a second account on my iMac, and try playing video there. It worked. No problems at all. Weird.
So I started looking at differences between the new account, and my standard. I'd already made sure nothing unusual was running, and no processor hogs (not that anything short of Handbrake at full settings has come close to pegging out the processers on the new box). I found one thing, that made a difference. I had Timemachine backups, going to the same Drobo FS (though a different partition) turned on on the iMac.
Timemachine was running the whole time, and didn't impact any other streaming from the same machine, but it did make iTunes video playback of 1080p movies skip like my 6 year old daughter on the iMac. I turned it off.... no more skipping. I've watched 5 TV shows and 2 movies on that account, and not had another single incident.
Obviously, there is still a problem. The iMac and Drobo have enough bandwidth that they can do all the work at the same time (or I'd be seeing the problem on the other devices while streaming), but they are not playing well together on the same account. I've also checked the throughput to the Drobo FS from the iMac... way more than necessary. If it were a read / write thing on the Drobo, then I'd expect other devices to see the issue when I'm watching something on the iMac that is skipping, but there was still no skipping on any other device at that same time...
But, as I said, I found the root cause in my case. I can turn off Timemachine backups while I'm watching a movie on the iMac, or I can move where I write the Timemachine backups to (going to try this over the weekend to be sure it works). If moving the Timemachine backup to a different drive doesn't work, it's a bigger problem.
I'd really love to see Apple fix this and the issue where I have to turn iTunes on in 32bit mode when using an external library (of it gives the funky quicktime error until you delete and readd the movie).
Hope this helps some of you, if not all.