Just thought I'd give an update......
We let the floor dry out for several weeks, had the plumber in to discount any leaks from the supply side (which he did), bought a moisture meter (which showed that the dark patches were indeed damp) and scratched our heads (again).
There is no obvious movement of tiles, either on the floor or the walls, and no cracking of grout. Thinking things through logically, we came to the conclusion that perhaps the water that was appearing beyond the shower screen was indeed the water which had got underneath the shower tray when it was first installed (when there were bits of grout missing round the drain and tiny cracks in the floor grout, before we re-grouted with epoxy). Apparently it can take up to six months for this water to dry out completely, and of course it was having to travel further (beyond the shower screen) to evaporate as we had re-grouted with epoxy in the shower area.
So, armed with moisture meter readings, we started using the shower again.
Remarkably, the damp patches did not become even damper, and, even more remarkably, over time they have completely disappeared. Admittedly, for the past month or so we have had the underfloor heating on, but we also had it on in order to try and dry the tiles in the summer, and it didn't seem to work then. So it appears that, perhaps our theory is right, and that we just had to play a waiting game. In all, it probably took around six months for the water that originally got under the tiles to find its way out.
The epoxy grout seems to be holding up fine, with no signs of cracking at all, and we have made sure that we have a good Silicon seal along the bottom of the shower screen so that the main shower area is entirely waterproof above the tiles. Yes, we still have normal grout up the walls, but if there was any significant ingress of water coming from there, I think we would still have problems with the floor being wet, which we don't.
It is still a mystery to me why so much water was able to get under the tiles in the first place....I can only think that the grouting was done badly, as there was never any movement of tiles on the tray. It certainly never looked really bad, but having been done very carefully with epoxy the second time, we have not had any further problems.
So, as I said before, I am a big fan of epoxy grout in shower trays. Given how easy it is to allow excessive water to get under the tiles and perhaps travel beyond the shower area, I can't understand why it's not
standard practice to use it for wet room showers! If we ever have one done again, I will definitely be asking for it over the whole floor of the bathroom.
Of course I'll keep you updated if things change!