I had the same problem you do when I upgraded my HDTV and AV receiver to 3d capable. I was running fine with standard Blu-Ray playback but had excessive stutter when playing 3d content. I hate to tell you this, but you really need a graphics card that supports 3d Blu-Ray with hardware acceleration - otherwise its pounds your CPU. My card supported standard BD HW acceleration but when I played 3d, I found my CPU was pegged. Take a look at yours while playing and I bet it's the same issue. Both Nvidia and ATI say they're "3D Blu-Ray compatible" for a bunch of models of cards but what they don't say is that only certain cards support the dual stream hw acceleration for 3d BD. When you think about it, 3D is really putting out two hidef streams simultaneously. I upgraded my older card to an Nvidia 550ti which supports it and the problem is gone - my CPU is hovering around 5% now. Here's the nvidia page showing their models that support 3d with HW acceleration:http://www.nvidia.com/object/3d-visi...rce-cards.html
In the dropdowns, choose "GPU Series" on the left, and "3D Blu-Ray" on the right
Oh, and PDVD ultra and Corel WinDVD do actively use the GPU's hardware acceleration for 3d if the card has it. Otherwise, it goes to your CPU to support it. I have both but I almost always use Corel just because I found it easier and less bug prone.