Some slideshow modules or other fancy modules will not work properly when placed through Modules Anywhere.

Some javascript based modules don't like to be placed any other way than through a module position. Which is quite understandable, frankly.
Modules Anywhere outputs the modules in areas where they shouldn't really be (they not designed with that in mind at least).

So modules that rely on javascripts might not work, because they can't place the scripts in the right way or something.

Also some modules (also javascript based ones) don't like to be placed more than once. These won't work either if you place them twice on one page using normal module positions.

So try to not have the module in the side or somewhere if you want it in the article.

In case you have some javascript based module tahat only works if you DO have it already somewhere on the page, the workaround is to place the module in a hidden module position.
Make a new module position in your template called 'hidden' or whatever, and wrap it in a hidden div.
To do that, add this to the bottom of your templates index.php (above the </body> and debug module tag):