That's completely understandable not wanting to provide urls in a public area, but in this case, I already know what the issue is that you are running into.
The exclude current page setting should be working fine, and it seems that's not the case. The real issue lies with 'exclude duplicates', and there is a good reason why, especially in the manner that you are using it. The 'exclude duplicates' only pertains to the APL plugin.
Whenever the plugin is used, each time it gathers the posts that it is going to display for a preset post list, it will also store the post IDs in the class variable. So, from the time it is first used on a given page, the post list itself, has the option to exclude those post IDs that the APL plugin has already queried. Which means, any other function and/or plugin that is outside of the APL plugin, will not be stored in the class variable exclude list.
Creating your own WP loop creates a function that is outside the APL plugin, and isn't added to the exclude list. The exclude functions probably could use some more enhancements like excluding post IDs by created post lists that you don't want repeated, but for now I created a way to exclude any duplicates that may be created by the APL plugin on a given page.
I would be interested in how you are using the plugin though, and what tasks you are trying to accomplish. Kind of gives me some ideas from time to time for future enhancements, but I guess that would be up to you if you want to share.