Handbrake Encoded Video Stutters in iTunes

[thunderclap]

I have a Windows system running the latest iTunes. I've been encoding my DVD's and Blu-Ray's using the AppleTV 3 in Handbrake. The DVD encoded files play fine across the board, but the Blu-Ray are another matter.

I'm encoding the files in 1080p using the AppleTV 3 preset. Now, the videos play fine when streaming to my iPhone 4s and AppleTV 3 but when I try to watch them in iTunes they stutter like crazy. I've tried playing the same files in VLC and Windows Media Player and they're fine, so it's something with iTunes.

My system is a Core-i5 3.4GHz Ivy Bridge with 16GB RAM so there is definitely more than enough horsepower to handle this. Any idea why iTunes struggles?