Searching for this exact problem... not a SW user, but I've got RW 3.5.1, Win 7 Pro 64 bit, 32 GB of RAM and AMD FirePro W5000 workstation graphics card.
I believe there are two steps required for this. First I did as outlined above, then also increased the acceleration of the 3dconnexion mouse explorer fpr panning and zooming.
The next part was I noticed some settings in the Rapidworks in File -> Preferences, Tolerance tab, there is a "Maximum Radius of Analytic Shape" which was set to 1300 mm. My model is bigger than that, which explains why when zooming, parts of my model would disappear.
Then in the Hardware tab that seemed like they could be tweaked, so I changed a few things to "Hardware". Note that "Use video RAM for Rendering Acceleration" in my case made the model disappear when not in motion.
Ultimately, I'm using a combination of the 3dconnexion explorer and the normal mouse wheel for zooming in and out. And when the model flies off the screen, I CTRL+F to re-center it.
From my experience using the 3D mouse in Rhino 3D, I believe the 3D mouse will occasionally move or reset the origin of the view. In Rhino, touching the 3D mouse presents a blue circle where this origin is. I've noticed similar behavior in Rhino when the circle has jumped: any input makes the model move off screen rapidly.