When you set up your activity (i asume you call it "watch tv" or something like that) on your harmony elite, at some point it will ask you "With which device do you switch channels?". maybe you selected the tv instead of the tv box?
To test this, do this: Go to "devices" on your harmony elite (it's an on-screen button on the remote). There you can select the sunrise tv box. Once selected, the remote control is now focused on the tv box. Can you control the tv box now? if yes, delete and re-program your "watch tv"-activity. if not, than i would guess that something went wrong with the setup of the dongle, and i don't think i can help you there...
Also: make sure that there are no obstacles between your flirc dongle and your harmony hub, or harmony elite (if your not using a hub). Infrared does not penetrate physical obsticals very well :) in the end (if it works) you can buy a usb extension cable, so you can postion your flirc better.
if you are using the hub, know that it is the hub that communicates with your devices, not the remote directly. the remote sends the command via RF (radio waves) to the hub and the hub then uses infrared, bluetooth or wlan to control your devices.