The sample file annotationHandler.php needs to handle both a GET request and a POST request. If the annotations aren't being loaded into the viewer then maybe the GET request isn't being handled correctly. When a GET is made your server should be returning the XFDF string of annotation data, so that's where I would check to see if something is going wrong.
If you want to debug and see what your server is returning to WebViewer you can add breakpoints to BaseReaderControl.js inside the callback function passed to this.docViewer.setInternalAnnotationsTransform. You'll see a call to $.ajax and either the success or error callbacks should be hit.
Matt Parizeau
Software Developer
PDFTron Systems Inc.