I imagine this has got something to do with the TRUST code, although it's unusual to see it used for passenger trains; it normally only happens with freight.
For example, from the Euxton Jct page, this freight is running as 493Z, which is part of the TRUST ID: http://www.realtimetrains.co.uk/train/H90828/2014/04/09/advanced
Which train is in the picture, so we can see what's happened to the TRUST code on the RTT page?