No, you misunderstand. My gems don't work was not because they were stacked. They simply don't work because the game(RoS) no longer recognise the affixes on gems
I mod 9 gems at a times and I only mod the gems that are in my bag. This way I can make sure no modded gems are stacked. So what I did was put 1 of Ruby Tier 16, 15 and 14 in my bag then I do the same for Emerald and Amethyst.
After the first 9 gems is modded, I went in game and socket them into my gear piece. The modded affixes stay. Everything was working as expected. Then after that I pull out another 9 gems from my stash and put them in my bag. Same concept. No gems are stacked since they are from different tier.
I do this until I sockets all the gems into every single gear piece(13 pieces = 36 gems to sockets) Everything went perfect as I expected. My character achieved all the stats that I said earlier.
Now, the disappointing part.
I log on PSN to use the EXPORTING SAVE feature. Again, exporting save was fine. No error whatsoever.
Now I turn on PS4 and do the IMPORTING SAVE. Again, save was imported successfully. I went in game and BAM! Those mouth watering stats that I modded in PS3 are gone. It's like they remove the affix address of the gem entirely.
Imagine the gem has a box where you put all the affixes in it, they just remove the whole damn box. And if this the case, we can say goodbye to modding gem in RoS