OK just a guess here, is it possible that these tiles are from a different batch? Were the codes checked? Do you remember the order of fixing them? did you place the tiles where the shower mixer is as you went? or left them till the end?
As I say this is just a guess, but is it not possible that the tiles have always been a different colour (if from different batches) and that it was not noticed at the time of installation, as when they were fixed to the wall the wet adhesive made the all the tiles appear uniform in colour but as they have dried they have returned to there original colours?
just a guess???
Also, the tiles in question are the ones most at risk from getting water behind them. shower tails cut through the two full tiles and the two at in the corner which is where water will pool, it also looks like it is traveling up the wall in the corner. But you say they are bone dry so confused