Some webpages, such as content management systems, may not work in tandem with iAnnotate’s integrated browser. In these cases, the downloader cannot "detect" the PDF links and displays them in the integrated browser, or the website doesn't work properly in iAnnotate's browser.

In this case, you can use "Compatibility Mode" (under Advanced Settings -- or use the "Compatibility Mode" option from the Action button in the integrated web downloader). In this mode, almost all websites work in the integrated browser. However, instead of auto-detecting PDF links, the browser will open up the PDF files directly in the downloaded window. When you have such a PDF loaded, tap the action button and use "Download PDF" from the menu in order to add the embedded PDF to your Library.