iAnnotate can transmit documents as flattened or non-flattened. Flattened documents have their markups compressed directly into the document, meaning those markups can be viewed in most desktop (Mac/PC) programs and mobile (iPhone/iPad/Android) apps.
Non-flattened documents, however, have annotations that basically "float" in a separate layer on top of the document, and because of that structure, they usually won't display properly in external mobile apps or in desktop locations like Google Chrome or on the Dropbox/Google Drive websites.
Comparing Your Viewing Options
Syncing a document in iAnnotate PDF updates it with non-flattened markups. The best place to view it is on your Mac/PC. Native desktop programs like Preview or Adobe Acrobat/Reader can render and display the non-flattened markups very well. However, other desktop sites and programs may not have the ability to render editable annotations.