Storyline 3 course not loading correctly in LMS unless the player is set to launch in new window

Storyline 3 course not loading correctly in LMS unless the player is set to launch in new window, but then we have the issue where there are two screens appearing, one with a launch button, and one with the actual course.

We are publishing to SCORM 1.2 html5/flash and loading into ISOtrain lms.

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