There must be something different in your own localhost version of this module vs. the released code, because following the installation instructions for 6.x.-1.0 causes the $messages to show up on the page twice!
I pasted your example php from the installation instructions:
<?php if ($show_messages && $messages): ?>
<div id='console'>
<?php if ($show_messages && $messages): print $messages; endif; ?>
</div>
<?php endif; ?>
Into the page.tpl.php of my custom Blueprint subtheme, wrote a basic drupal_set_message('You have made an error!', ''error'); into the template.php's template_preprocess_page() function, and then refreshed my browser two times. I see the messages being printed to the page AND into the <div id="console">

I then tried some troubleshooting, such as commented out the original place where I had been printing the $messages, but they still show up twice. How were you planning to neuter the $messages array so that it didn't get printed to the page, but only to the console div?
Comments
Comment #1
slantview commentedHey Joel, you need to comment the print messages out in the original place where the messages appear in all page*.tpl.php files. Sorry if I wasn't clear about that. I want to try to find a more elegant solution, but I thought this was a good starting place.
I'll see if I can find a better way to neuter the messages before they get to the page template.
-s
Comment #2
senpai commentedSee, that's just the thing. The *only*
print $messages;on the page is the one from your instructions. I don't see anything in the module, the js, or the CSS that would alter this bahavior, so I'm stymied.Please explain the theory of how it's supposed to work?
Comment #3
mileZ commentedI've the same issue.
Comment #4
wuf31 commentedYep, I also have the same issue.
Comment #5
lelizondo commentedSubscribing
Comment #6
fricike commentedYou can hide the original messages box:
Comment #7
lelizondo commentedNice solution, is working for me. Thanks.
Comment #8
wuf31 commentedplease don't set it to fixed, unless the maintainer has merged this into his code.
Thanks for the fix, haven't test it though..
Setting to reviewed & tested by the community as per lelizondob comment.