Figured it out! The Hype projects weren't playing nice inside Bootstrap's main 'container' div, though there didn't seem to be any conflicting js or css in my developer tools. I'm going to guess that Bootstrap's percentage-based scaling might have clashed with Hype's? And maybe only in Dreamweaver's version of Bootstrap...anyway, added some min and max heights to my Hype divs and kept them outside Bootstrap's 'container' divs and boom! They appeared and worked swimmingly!
Sorry I can't think of a good technical explanation (not that talented) , but it seemed as soon as I put my flexible layout Hype divs inside a Bootstrap div they would render with 0 height. Outside, totally fine. Hope this helps anybody else with this issue!
Thanks for your help Michael, I should probably read your book!