We use a waterbased Teflon (Kevin martin can get hold of it) it's breathable and fairly resiliant to being applied on damp substrates…although you do need to be sensible.
The problem I see from that image is sandstone is pourous and the water is being "wicked up" from below evident from the "damp" stains you can see,these areas will "go mouldy" from the inside . You also have problems with it going green from above…normal things that affect paving shade,bad drainage,type of stone etc.
I would say it has been layed on a wet mix…tap the flags .Do some parts sound hollow?