I've had this issue for a little while and cannot figure it out. It started on my old server (q9550 + 8GB) and has followed me to my new one (2x Xeon 5450 + 24GB). I've done a complete new install of Emby on the new server to make sure it wasn't a setting that I configured and forgot about.
It happens with any 1080p videos (over 300 movies). It worked before but I don't know what has changed. If I open the web player (even on the server itself) and try to play a video at 1080p it just sits there doing nothing. There's no process change on the server. If I change the quality to 720p it plays just fine.
Using Google Chrome as web client
2x Xeon X5450 (8 cores @ 3.0ghz)
24GB DDR2 667
Windows Server 2012 R2