Yes, LTAF needs to hook into the window.open of the test page, and this happens whenever a command is received by the driver frame. If you navigate to a page that automatically popups a new page, LTAF doesn't get a chance to capture it.
BTW, there is a known issue in the current version that if a test fails while automating a popup window, the DOM that is reported in the error page is from the main window instead. We are looking at addressing that in the next release.
- Federico