The "OK" button of an Alert dialog should be automatically clicked. Do you think the default timeout of 5 seconds is sufficient for your scenario? If not you can just change the HandleTimeout step property to a bigger value.
If that doesn't help can you please elaborate more on how the application behaves? For example you type some text in the main application window then click a button which pops up an Alert dialog, is that the case or is it more complicated?
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