Why does my sky+ show different strength for the two inputs

Before you do too much, try swapping the cables between the 2 tuners, just to make sure, I have 2 Sky Plus boxes here, and a couple of combo boxes. all running on a multiswitch system, so the LNB is isolated from the boxes. One of the boxes shows a difference between the signals, and if I swap the cables over, the signal strength doesn't change, for whatever reason, the tuners in the box are different quality.

That said, a faceplate on the wall will degrade the signal some, but it shouldn't make that much difference, unless there's something else going on with either the LNB or the cables. Some of the cable used a few years ago wasn't the best quality, so that might also be a factor.

Another possible is that some water has got into the cable, and is attenuating the signal. if the cable comes over a sharp edge anywhere on the way down, over time, especially with weather like we've had recently, the cable outer insulation can be abraded, and that can then allow the cable to fill with water, to the extent that eventually, it will start dripping on to the floor, or even short out the cable completely, stopping the LNB from working correctly on that channel.

And yes, the recent very high winds may have moved things slightly, perhaps enough to upset the signal quality, the receiver signal strength indicator is usually as good a way as any to set the dish for best quality.