There seems to be a font-size: 0px; getting added to the style sheet that gets injected into the code at every instance of the shortcodes, for the master div.
Overruling that with a localized font-size style declaration on the disappearing element makes it reappear.
Should that be there in the code? Should we just hack the plugin file where it’s injecting the font-size: 0px;? Remove that attribute? Change it to ‘initial’ like the plugin does in the next few style lines?
IE seems to be taking the font-size 0 literally and hiding this content.