Your code uses the axes handle "handle.axes1" for plotting. But either "handles" should be unknown, the axes should have been destroyed before, or you draw to the figure created by GUIDE, if this is open. In most cases an error message in the command window should reveal the problem.
The solution is easy: Create the wanted axes obejct manually:
axesH = axes;
X = [1 2 3; 4 5 6; 7 8 9];
plotmatrix(axesH, X);
