Looks like it's an issue in how vimeo now handle's video embedding. Rather then trying to use iframes, which is how their current embed code works, I needed to directly link to the source based on the old embed code (which vimeo no longer supports). The HTML5 video player doesn't appear to function within filemaker, even though loading quicktimes directly work's fine.
Here's my code incase anyone else needs it in the future. It's set directly as the URL for the web viewer and "Projects::videoID" is the vimeo specific ID of the video which can be found in the main URL on vimeo's page.
"http://vimeo.com/moogaloop.swf?clip_id=" & Projects::videoID & "&force_embed=1&server=vimeo.com&show_title=1&show_byline=0&show_portrait=0&color=00adef&fullscreen=0&autoplay=0&loop=0"