I think the problem you're seeing is a result of the fact that plotmatrix sets the figure's NextPlot property to 'replace'.
For clarity, here's a small example that illustrates the problem as I understand it:
f = figure;
a1 = subplot(2,1,1);
a2 = subplot(2,1,2);
x = randn(50,3); y = x*[-1 2 1;2 0 1;1 -2 3;]';
plot(a1, 1:10);
plotmatrix(a2, y)
So far so good, but ...
>> get(f, 'NextPlot')
ans =
replace
>>
Usually, that would say 'add' for a figure (that's the default, anyway). So with that property set to 'replace', the figure essentially deletes all its current contents before anything new is added. That's why if you now do this...
plot(a1, 1:10);
... you'd see the plotmatrix plot go away.
To work around this, you can manually set the figure's NextPlot property after calling plotmatrix:
f = figure;
a1 = subplot(2,1,1);
a2 = subplot(2,1,2);
x = randn(50,3); y = x*[-1 2 1;2 0 1;1 -2 3;]';
plot(a1, 1:10);
plotmatrix(a2, y)
set(f, 'NextPlot', 'add')
Now you can re-do the plots without error:
plot(a1, rand(5));
plotmatrix(a2, rand(3))
set(f, 'NextPlot', 'add')
