How are you trying to "identify" these annotations?

Also, it is recommended that you use the WebAnnotationViewer's AnnotationClicked event if you are trying to execute a function when an annotation is clicked.  Here is a sample:

atalaInitClientScript('OnPageLoad();');

function OnPageLoad(){
   WebAnnotationViewer1.AnnotationClicked = OnAnnotationClicked;
}

function OnAnnotationClicked(e){
   var clickedAnno = e.annotation;
   // Do stuff
}