You need to either sort it on your box yourself using Menu, Channels, OK on add fav's, pin 0000, in there you will see Popular=Red Entertainment=Blue Movies=Green Sports=Yellow. Highlight the channel and press one of the colours to select which category you want it to appear in. Or download a CDF already sorted for your provider / area. Did you not save your CDF before flashing.....
You would put your CDF back to your box after you have flashed it then done a factory default, put the box on standby when transfering the CDF.
AFTER you flash it as you are restoring the prefs you saved befor e you flashed (you did save your channels prefs didn't you ?) One of the quirks of the new FW is that it doesn't seem to let you edit the CDF file anymore.
There's an edit button true, but if I click on it the program crashes - on every file I've tried (Win XP). I have to edit using the old version of the software from 10/04, so it's not a big issue. Maybe works on different systems.