In terms of ports there are two separate ports. The CatDV desktop application connects via RMI to port 1099 and the Web Client (and other HTTP based clients like the iOS Apps, Premiere plug-in etc.) connect with HTTP on port 8080 by default. I wouldn’t change 1099 to 8080 that would probably cause confusion.
It does appear that there is currently a problem on Mavericks with the Control Panel persisting its settings. We are working on fix for this it at the moment, but that might be the problem here. Not that it should actually stop the server working, it will just show up wrong in the control panel.
I would suggest that if you are still having problems that you email support@squarebox.com and we’ll investigate further.