Where are you placing your map.infoWindow.resize code? Is it within a dojo.connect for each layer? I'm doing this with version 3.3 of the API without any problems: //Listener event for feature selection and the popup info widow
dojo.connect(theUsgsLayer,"onClick",function(evt){
//Listener event for feature selection and the popup info widow
var query = new esri.tasks.Query();
query.geometry = pointToExtent(map,evt.mapPoint,15);
var deferred = theUsgsLayer.selectFeatures(query,esri.layers.FeatureLayer.SELECTION_NEW);
map.infoWindow.resize(350,300);
map.infoWindow.setFeatures([deferred]);
map.infoWindow.show(evt.mapPoint);
});
//Listener event for feature selection and the popup info widow
dojo.connect(theFloodplainLayer,"onClick",function(evt){
//Listener event for feature selection and the popup info widow
var query = new esri.tasks.Query();
query.geometry = pointToExtent(map,evt.mapPoint,15);
var deferred = theFloodplainLayer.selectFeatures(query,esri.layers.FeatureLayer.SELECTION_NEW);
//map.infoWindow.resize(map.width * 0.70, map.height * 0.6);
map.infoWindow.resize(200,175);
map.infoWindow.setFeatures([evt.graphic]);
map.infoWindow.show(evt.mapPoint);
});