Apps that use the jquery fancybox plug-in in iframe mode exhibit clearly wrong behavior in Native App mode. You can see this in the LucidCharts app currently in the Apps developer preview store, or by running the fancybox iframe-mode demo at http://fancybox.net/
Wrong behaviors are visible as a result of this in LucidCharts "tips" popup; the close button causes a refresh of the page (instead of closing) and the "skip tips" link causes the window to close (and the application to terminate). Passing of function calls from the interior iframe to the parent page appears to be implicated.
Needs to retested again on the new code for FF 14.
Do not get a reproduction of this issue with the web app runtime with fancy box demo with the new implementation.
Does not look like this is valid anymore. Did not see this happen with lucidchart.