When you enable permalinks in WordPress, it creates an htaccess file in whatever directory it’s located in. Since WordPress is installed in the root directory, there will be an .htaccess file there that enabled permalinks.
It is possible that the rewrite rules that WordPress is producing are interfering with your install of ecommerce.
If ecommerce doesn’t use an .htaccess file in the directory it’s installed to, you can create a blank one in the ecommerce folder.
You may need to add this to your .htaccess file
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /ecommerce_folder/
</IfModule>
This will prevent whatever rewrite rules wordpress is using from affecting that folder.
You may also want to see this post:
How to avoid wordpress permalink rules to inherit in a sub-folder