I've been using Hype to replace Flash animations/interactive content in the D2L Brightspace learning management system (LMS).
When a page longer than the screen is opened in a new window the page keeps scrolling to the top of the page so you can't see the content below. My workaround was to create a second 'dummy' Hype document (32 pixels wide by 1 pixel high, with a rectangle on it the same size) to sit below the main Hype content. This stopped the page from scrolling to the top. Not sure what the cause of this is but if I find out, I'll post back here.