Even I ran into the same problem. After several hours spent with selenium, a solution was found for handling warnings and tooltips in a java script.
we can use keyPressNative selenium to handle java script warnings from RC selenium.
Here's how the method should be used key*Native():
selenium.keyPressNative("27");
selenium.keyPressNative("10");
selenium.keyDownNative("16");
selenium.keyPressNative("79");
selenium.keyUpNative("16");
selenium.keyPressNative("67");
Not recommended, but helped me deal with some of the failures of selenium.
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