Hi there,
We haven't had any reports of this happening.
Do you have any other software on those sites? Because some Article Manager directories have full write permissions, if someone can gain access through any other program, they can write to Article Manager directories (or any other directory with write permissions.) So, something can appear to be related to Article Manager, while actually being the fault of another script. (This actually happened to me once with an outdated version of Wordpress on an entirely different domain than where the malware actually appeared. Drat!)
If you'd like us to take a look into it for you, feel free to fill out a support request:
http://www.interactivetools.com/support/email_support_form.php