Inconsistent Formatting Published HTML

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I publish a lot of results in html, but often have trouble getting text and figure to appear at the proper place, or at all.
I know of "snapnow" and "drawnow", but they give varying results, sometimes worsening the problem when called inside nested functions (I think).
Does someone have a robust way of getting text and figures to appear inside the proper chapters?
(I often use if-then to exclude certain chapters from running.)
Below a few examples of issues:
  1. Chapter titles outside an if-then statement mis-places text and figure vanishes
% main example 1
if 1
%% chapter 1
t = 1:0.01:10;
b = sin(2*t);
figure;
plot(t,b,'b');
disp('hello world');
end
%% chapter 2
if 1
figure;
plot(t,2*b,'r');
disp('hello world 2');
end
if 1
%% chapter 3
figure;
plot(t,3*b,'k');
disp('hello world 3');
end
2. Duplicate images.
I couldn't quickly reproduce this in an example. It seems to occur only in longer files with lots of nested functions so I couldn't pin-point the problem there.
Any help is appreciated!

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