We are having a problem with our SKy+ box at the moment, and this time rebuilding the directory, or indeed doing a full reet of the box did not help.

The symptom is reasonably simple - the box does not respond very well to the remote control, even down to the red LED not responding to keys being pressed on the remote control. After a full restart it work for a little while, then goes bad again.

So as a last ditch effort before I try to put in a new harddisk I tried this:

if the problem persists disconnect the digibox from the mains power. Press and hold the 'left' and 'right' navigation buttons on the front of the digibox whilst you reconnect the mains power. Continue holding the buttons in for about 20 seconds, and when the ring of light on the front comes on, press the 'select' button on the front of the digibox (between the left and right buttons you were holding). The Sky+ recording logo lights will spin backwards and, according to the Sky engineer, this will "clear the hard drive".
Once this is done, disconnect the digibox from the mains power again and this time press and hold the 'back up' button whilst you reconnect the mains power. Continue holding it for about 15 seconds until 3 lights on the front of the box come on and you get a full-screen message saying "Updating system software. Do not disconnect mains supply or satellite dish."

[From Sky Plus system fault, how to fix faulty Sky+ without £65 callout fee @ PaulAnnett.co.uk]

And it worked better than the previous solutions I tried - so let's see if it "stcks".