This problem started for us a couple of weeks ago too, when we had no channels at all one evening. After initially calling Sky and booking a technician for the next day, I checked again later on that same night, and it was working again. Checked again the next morning and all channels okay, so I cancelled the engineer as I figured whatever had caused the problem has righted itself. Then noticed a few days later that some channels were working, but some not, so wondered if the dish had got out of alignment - bought a satellite finder, and confirmed with that the dish was okay, and the LNB was set properly. Double-checked all the cabling, and confirmed no problems there.
To make things more confusing, it would either be no channels at all, roughly half of them, or all of them (generally only this in the evening though). During the day we could even be watching one channel fine, switch to another channel that gave a rain-fade message (despite clear blue sky!), so go back to the original channel and find that had now gone to rain-fade too!
So giving up on resolving it myself, called Sky again, and the engineer turned up next day. Explained the problem to him, and I recall he specifically asked if the channels were better in the evenings which gave a hint that he'd seen it before. The problem? Water in the LNB! Despite having drain-holes, if these get blocked and water stays inside the LNB, during the day, when it's warm, the water tries to evaporate, but can't escape properly so mists up the inside of the LNB and gives a rain-fade message. In the evening as the temperature drops the water condenses again and falls to the bottom of the LNB, clear of the receptors, and all channels work again!
Perfectly logical really, and with a new LNB installed all channels worked perfectly. This may not be the solution to every occurance of the intermittent reception problem, but I thought it's a useful answer to know about, which may prevent a lot of confusion!