1 set of (Current day design) Emeralds pre Chaos rampage in Tikals time.
Chaos absorbs negative power in said rampage, leaves behind one set of gray emeralds (just like in the Super Sonic story in adventure.) Tikal does her poetry thing, Master absorbs Chaos, and in so doing causes the negative power of the emeralds to 'Chaos Control' in to the special stages.
So after Chaos has his tantrum two sets of 7. Negative energy set in the special stages, positive energy set at the alter on Angel Island. Make up a reason for them both to regain their colour and hexagon shape as seen in games 1 2 and 3.
'Positive' emeralds sit on Angel island for a milenia or so. The ancestors of Knux get somewhat attatched to their gems.
The negative set travels through the special stages and go on lots of adventures, they learn to live, to love, and how to destroy most people who find them, including the people on Westside Island, South Island, the Gizoids creators, a bunch of birds that loved Skateboarding so much that they decided to make a magic carpet(Riders), and the like.
Eventually the negative set is found by a certain blue hedgehog whilst rolling about South Island. And for one reason or another the 'Chaos Control' back to the special stage after changing the colour of a few Sunflowers. Destroy the world, give Hedgehogs a hair dye, flower arranging, those emeralds can do it all.
Sonic gets all the negative emeralds again on Westside... but turns Super. This bit I admit is probs fanwanking, but Sonic turning Super with the Negative Emeralds effects the Positive ones. The Emeralds Knux has, as stated by some Japanesse manual (3? or was it S+K?)explode. I guess the energy was absorbed by the Master. Eggman lands and says a wizard... I mean Sonic did it.
Sonic3 happens. Knux does the most powerful move ever shown in a Sonic game and beats up a Super form. He steals what he believes to be his set of Emeralds. I presume the Negative set looks identical to the Positive set.
From there more fan wanking... Knux after stealing the Emeralds immediately witnesses something similar to the Sonic1 good ending. The emeralds end up in the special stage again.
Sonic gets em back, cue Sonic3+K. Sonic reunites the Positive, Negative and Master Emeralds. This forces Sonics set to become the Modern day shape emeralds, but still grayed out just like, again, in Adventure. More special stages release the positive emerald energy which was still in the master emerald from the ending of Sonic2, into the now standard Chaos, (but at the time Super) Emeralds.
1 set of Emeralds again.
Course there is alot of fan wanking to be done to clear little things up. Like the 6 emeralds in the first game thing. Geralds Journal in 'Battle' claims he found an emerald somewhere. One could say taht with that emerald he made the deus Ex Machina from Adventure2 and Shadow, and the emerald was some how reunited with the others during the chaos control at the end of Sonic1. Or that Rings were created when Chaos had his rant, and the emeralds split and scattered all over, and thats why the two objects are connect so often.
Oh and form 'legends' saying the emeralds were hidden on South and Westside island... We know they were not. Emeralds were not hidden there... Gates to the Special stages were.
...Lol at how bord I must be to type all that on this subject. I am going outside now.