I came across a similar question on Stack Overflow about IE rendering inline-block div differently than FF/Chrome, but unfortunately it didn't provide the solution I needed.
Below is the CSS code for my element (which appears as an invisible square link in HTML):
#box-scenario {
position: absolute;
margin-top: 43%;
margin-left: 37%;
background-color: rgba(255, 0, 0, 0);
width: 11%;
height: 21%;
display: inline-block; }
The positioning of this invisible square link seems to be around 200px higher compared to FF/Chrome.