Michael Tallhamer, MSC, DABR
Do you have the remotes that go along with the AlignRT system? If so check and see where the remote receiver is placed (typically on the back wall or mounted just above the pod 3 camera).
During my testing I found that the remotes experience interference if the receiver is in the path of laser guard. There is a chance that laser guard is causing some type of issue in combination with that receiver if you have it. You can cover the receiver with something and see if it is the issue and then have your service engineer move it to a new location if that ends up being the case.