Blame Apple for the lack of a Quicktime XDCAM codec on Windows...
How many layers results in "stuttering?" Two? Five? Ten? If you're talking about five or so, that's probably due to a hard drive bottleneck issue; even though the compression is pretty high on XDCAM (35mbps), multiple streams can add up quickly and lead to stuttering on a single drive. Beyond that, XDCAM is MPEG2 compression, and so that incurs some processor-overhead to decode (even the native files would suffer this).
However, if it's only a few clips, you've probably come up against the limitation of 32-bit QuickTime support. Adobe had to develop a translator of sorts to enable QuickTime playback (which is still 32-bit on Windows; again, thanks Apple) on the 64-bitness that is Premiere Pro CS5. There is some overhead involved in this on-the-fly conversion, so that may be a factor in the stuttering.
You could tried batch converting the files to DVCPROHD using AME; AME will create a P2-compliant folder structure, and while the bitrate is higher on DVCPROHD (100mbps, though actual muxed rate depends on the format of the DVCPROHD you encode to), there is less processor-overhead needed. It's going to be a case of "six of one, half dozen of the other," I'm afraid. You could also consider an offline workflow, where you transcode to something more editable yet, like DV, and then swap out the DV files for the XDCAM files later.
Thanks for those insights Colin. Yeah, I've learned that a lot of this is due to the sometimes petty Apple vs Adobe & Microsoft battles.
My dropped frames were coming on just three layers with the XD Decode codec. Good call on the AME suggestion -- it seems obvious now and with the added codec it can definitely help with this. The resulting .mxf and .avi test files I've just created can do a dozen layers or more, though I found the mxf files 60% larger and avi's around 250% so that's the penalty.
I'll keep exploring. Luckily, this project doesn't kick into full gear until late October.