Capito ma a me in realtà interessava solo far funzionare il javascript, che non va 
Eppure ExternalInterface è attivo...
codice:
<mx:Application xmlns:mx="http://www.adobe.com/2006/mxml" creationComplete="start();">
<mx:Script>
<![CDATA[
import flash.net.*;
import flash.external.ExternalInterface;
import mx.controls.Alert;
public function start():void {
if(ExternalInterface.available){
Alert.show('ExternalInterface available');
ExternalInterface.call("alert('This is javascript called by flex on linux')");
} else {
Alert.show('ExternalInterface is not available');
}
}
]]>
</mx:Script>
<mx:Button id="button1" click="start()" label="START!" />
</mx:Application>