I have a similar problem, (occurs in 2009 and 2010 versions). Problem occurs after setting some axes properties.
Zoom works normally when running the following code segment.
newHandle = figure(numPlots);
newAxes = get(newHandle,'CurrentAxes');
However, after this line, zoom behavior changes.
With the new zoom behavior, single left-click does nothing, and boxing an area isn't allowed. To zoom in, you hold the left mouse button and drag up or to the right (down or to the left zooms out). Additionally with the new zoom behavior, sometimes double clicking changes the angle the axes is viewed, and changes zoom back to normal.
Clipping is on, i tried changing the order of the children in the axes, i tried using cameraUpVector rather than using view, and I tried moving the set() after the first plot.
Anyone know how I could either fix zoom, or change the plot orientation without messing up zoom?