The problem might be that UIAlertViews are shown in an other window, or like you suspect, the alert view is presented from another process which should be unreachable to the apps code. Is there a way to check for views in another UIWindow instance?
Update
As noted here: https://groups.google.com/forum/#!msg/kif-framework/iDBomK8kyL8/wLtlh80YrpsJ
As I understand it touch events are routed by iOS to a UIWindow, which is then responsible for dealing with them as it sees fit. KIF and friends use a technique where touch events are synthetically created and then sent to a UIWindow. Since your app code doesn't have access to the UIWindow which is presenting the alert box, your app has no way to send it a touch event.
Of course you can manually loop through the windows of the UIApplication with [[UIApplication sharedApplication] windows]
or use [[UIApplication sharedApplication] keyWindow]
, but I don't think the testing framework supports that.