This behavior extends to all installed Unity Web Apps using Chromium. After a fresh install of Ubuntu 13.04 the apps were working correctly and selecting a web app from the sidebar would result in an indicator icon appearing and opening the said web app. The following day selecting the same app would launch a Chromium icon that would appear separately from the web app icon and the Chromium icon that is locked on the sidebar.
I have attempted to upload an image but it seems that I do not have the required reputation, so I can clarify if needed. Is there any way I can remedy this?