Can you post some code to reproduce this?Have you set up an event listener to resize the map when it's content pane resizes? All of our samples that use content panes (quite a few of them!) do this with the following code:
dojo.connect(map, 'onLoad', function(theMap) {
//resize the map when the browser resizes
dojo.connect(dijit.byId('map'), 'resize', map,map.resize);
});