Don't worry Graig, you appear to have caught 'chud' on one of his more helpful days and I'm sure the Engineering and R&D staff at Sky and the broadcast equipment manufacturers would disagree with his 'unproven technology' accusation.
If your signal on all other channels is fine, then this is more than likely a problem with your box not believing you have paid Fuhrer Murdoch for the privilege of receiving his new glorious 3D. The Sky 3D signal is no different to their 2D transmissions - it is still a 1080i picture but with each eye recorded as a half resolution squeezed image on each side of the frame (hence side by side). All your Sky box does is to confirm with Sky headquarters that you have paid to receive the 3D service and if so it is then able to accept the signal and then decrypt it- it is your TV which is converting that picture into a 3D image (as per SonyCentre's instructions) not the Sky box. And as it is an ordinary 1080i signal, it is not due to any 1.4/1.3 hdmi handshaking problems.
If you tune into a 3D channel and leave your TV in 2D with the side by side image, does that pixelate after a couple of minutes or does it remain stable? If the side by side image remains unpixellated, then it is something to do with your TV's decoding, the 3D transmitter (inbuilt or external) or it could even be the glasses - do you have more than one pair and if so, does it do it on both of them?
Have you tried a system reset on your Sky box ? - it often works wonders on my Virgin V+ box (usually after I've kicked it when it has gone into its post 23.00 'You can press the remote as much as you want, but I'll change the channel when I'm ready, thank you' mode.).
Perhaps if none of these work or point you in the right direction, a call to Sky themselves may well be in order...
Rob