I have tracked down the problem to a cast in the EyeXFramework.Wpf.WpfCrawler class. The purpose of the class is to hit test and traverse the VisualTree to find elements that are EyeX interactors. There is an incorrect assumption that all the child elements in the tree are derivates of FrameworkElement.
I consider this a bug in the EyeXFramework for .NET that should be fixed in the next EyeX SDK for .NET release. Since it might take a while until the next release, you might want to go ahead and implement some workaround yourself in the mean time. (Remember, the source code for the EyeXFramework for .NET is readily available in the SDK).