I had the same problem before. The post is somewhat old, but I'll post anyway the solution for the case somebody else will encounter the problem.
h = rotate3d;
set(h,'Enable','on');
ax1 = subplot(1,2,1);
ax2 = subplot(1,2,2);
setAllowAxesRotate(h,ax1,true);
setAllowAxesRotate(h,ax2,false);
Working in this way resolved this problem in my case!
