If a test has a Handle Confirm inside an IF block and also outside any block, the one inside the IF block will fail:
Failure Information: 
~~~~~~~~~~~~~~~
Timed out waiting '5000' msec. for any dialog to be handled '1'
InnerException:
System.TimeoutException: Timed out waiting '5000' msec. for any dialog to be handled '1'
   at ArtOfTest.WebAii.Win32.Dialogs.BaseDialog.WaitUntilAnyHandled(IEnumerable`1 dialogs, Int32 handleCount, Int64 timeoutMilliseconds, Boolean resetHandleCount)
   at ArtOfTest.WebAii.Design.IntrinsicTranslators.Descriptors.DialogHandlerDescriptor.Execute(Browser browser)
   at ArtOfTest.WebAii.Design.IntrinsicTranslators.Descriptors.DialogHandlerDescriptor.Execute(IAutomationHost browser)
   at ArtOfTest.WebAii.Design.Execution.ExecutionEngine.ExecuteStep(Int32 order)

The dialog is actually handled, but the test is marked failed anyway.

If you disable or remove the Handle Confirm outside of the IF block, then all of a sudden the one inside the IF block works.