I've been running into the same issue now for the past few days. I had been fine running beta 14 with my SpacePilot using SW2012 SP4 at first after updating. However, the other day, I had my configuration start acting up, and the default profile started overriding all application-specific profiles, with SW being my main concern.
I got my SW profile to start working again by deleting the default application profile, but ever since then, I have had similar symptoms to the "stuttering" issue that Rift had described. My issue definitely seems to be related in some way to moving the 2D mouse shortly before or simultaneously with the 3D mouse. If I wait ~10 seconds or so after moving the 2D mouse before trying to use the 3D mouse, the problem will usually go away. System performance likely is not the issue, as I'm running this on a 6-core Xeon workstation w/12GB of memory and a Quadro 4000, and part complexity has no impact on how badly it stutters.
No other variables have changed that I know of, but it definitely was not an issue immediately prior to the previously described profile problems. I seem to remember having a similar issue at some point in the past (past year or so), but I cannot recall what driver version I was using, nor what I did to get it to go away.