I'm working in a staging site for this example problem, but the problem originated in the production site http://www.appdataworks.com. I've been able to reproduce the issue in the staging site after disabling all plugins.
I created a PopUp for a MailChimp form. No matter what I did, the popup would not work. I changed all of the settings so that the popup should show every time, and still, it didn't work. The site is on a GoDaddy Managed WordPress account so I Flushed the Cache, still no luck. Even with removing all site cookies it didn't work (I primarily use Chrome) and with a "delete everything on close" new browser session with Firefox it would not work. So I pushed it to the staging site.
I disabled every plugin except PopUp Pro, and BAM. The popup worked. So, systematically, one by one, I turned on each plugin, one by one, flushed the cache, cleared cookies, and tried loading the home page again. Every time the plugin worked until I turned on the Elegant Themes Monarch Plugin. That's when the Popups stopped working.
To be sure, I turned Monarch on and off several times and every time it was turned on, popups stopped working.
I've given you ADMIN Access to the staging site through the WPMU DEV Dashboard. Since it's your plugin that stops working when another plugin conflicts, I thought you should be the place to start. I've searched Google, WPMU DEV Support, and Elegant Themes support and found nothing.
You can reproduce this yourself, just load up the staging site:
and you'll see that a test popup comes up. Then go to the backend and enable Monarch, then refresh the home page. The popup will not load.
Thanks. I really need your Popup Pro plugin to work no matter what other plugins are installed.