Multiple servers don't work with Storyline output folder structure

I am testing my first Storyline course for a university, but the CMS - LMS structure we have appears to be preventing my project from working. I've published oodles of Captivate courses at other companies that use a true LMS, so both elements of this issue are new to me.

I have one video on a slide (originally an MP4 but has been converted to FLV for testing purposes) but the player doesn't find the video when we play it in our "LMS". I put LMS in quotes because it is not a true LMS. It's a combination of a CMS and a mocked up LMS player, which uses more than one server. From what I understand, because the Storyline player is trying to find a video in a subfolder of the published content, the CMS - LMS path breaks. 

Is it possible to alter the publish settings so the project is packaged into one standalone file? It's possible that if everything is one one root folder, it might work. 

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