This is probably because the axes scale is linear by default.
Change the 'YScale' property from 'linear' to 'log' as follows:
h1 = openfig('test1.fig','reuse'); % open figure
ax1 = gca; % get handle to axes of figure
h2 = openfig('test2.fig','reuse');
ax2 = gca;
% test1.fig and test2.fig are the names of the figure files which you would
% like to copy into multiple subplots
h3 = figure; %create new figure
s1 = subplot(2,1,1); %create and get handle to the subplot axes
s2 = subplot(2,1,2);
fig1 = get(ax1,'children'); %get handle to all the children in the figure
fig2 = get(ax2,'children');
copyobj(fig1,s1); %copy children to new parent axes i.e. the subplot axes
copyobj(fig2,s2);
Add the following:
set(s1, 'YScale','log')
set(s2, 'YScale','log')
