Inconsistent Formatting Published HTML

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!