The issue ended up being with the shortcode itself. I was displaying the poi body with the shortcode in the body, however, I was trying to reference a property ID that was different than what the other plugin was expecting – it’s a property management plugin. The shortcode was simply ignoring the ID I was giving within the individual properties’ maps and defaulting to that property. This made it look like the shortcode was working as intended for individual maps, but not in the mashup map – since it wasn’t a property page the shortcode didn’t have anything to default to. Maybe that will be helpful to someone in the future.
Regardless, you were absolutely correct about the initial tweak allowing for shortcodes within mashup maps. It is working just fine now with the correct ID list. Thank you for the great support and potential resolutions!