Ron,
Thank you so much for taking the time to respond. Your guidance helped solve my issue.
Although IE was not set to run in compatibility mode, the site which our Moodle is hosted from was unknowingly set to do so as a Group Policy Object. We removed from one machine to test and IE stayed in normal mode when the SCORM was launched in a new window.
We will this update org wide soon. In the meantime, I added the line you provided to the popup.php layout file. That worked perfectly!
Thanks again for your help; I really appreciate you taking the time to assist!