It is mentioned that Robotnik tricked Knuckles into thinking his emerald were stolen by Sonic... however that is not really reliable information.

It is also mentioned that the Master Emerald only starts to shine after the events of Sonic 3 & Knuckles, and that in the past (SA1) it dose not shine even with the Chaos Emeralds there because those event have not happened.

The Chaos Emeralds start at the alter with the Master Emerald with Chaos and the Chao. Go forwards to after Chaos attacks and Tikal use's the Master Emerald to stop him. This is the first time in recorded history that the emeralds have been used. So there is no reason for the Master Emerald to glow, if it's not being used. It glows later because it is being used at those times (like trying to keep the island in the air).

The Chaos Emeralds, are known to repel each other when all are together, because cause of this after the events of SA1(Past) they separated and at some point found by the Kitsune, a very advanced race. They used the emeralds for power but lost control of that power. Before their demise they placed six emeralds on an island to the south (south island) and kept one near their home (introduction of the seventh in Sonic 2)...(this also explains Tails being the only Kitsune seen in the sonic games)

...the Kitsune reference is from the japanese manual of Sonic 2.

Since the Emeralds have been away from the Master Emerald for so long (several hundred years?), when they are brought back to it they are powered up to their original form (Super Emeralds are therefore normal Chaos Emeralds). This is seen when the Emeralds from that point always have the 'diamond' like shape (however it is easily argued that looking at the Super Emeralds makes them look like the Chaos Emerald from Sonic 1-3&K, and therefore the older games merely looked at them from above and not the side).

Also the Chaos Emerald may not have neutralised the Master Emerald, that was Knuckles' opinion from what he saw/felt. The Emeralds' when together with the Master Emerald may have made some kind of connection to bring them all together. Although that is mere speculation, so to was Knuckles' dialog. He lived with the MAster Emerald all his life, NOT the Chaos Emeralds (which although similar are different)...(and remember, Tikal had conversation(s) with the Master Emerald, it may have some kind of instinct to gather the others)...(again, mere speculation).

As for the Mural, it could be seven went to the ground and seven stayed with the island... or just symmetry. Still interesting though.

Also, Knuckles couldn't call the Emerald 'Super Emeralds' since that name appears no where in the Sonic Universe history, merely in a screen to congratulate the gamer on getting one of them.

The reason the Island does not take off into the air when Chaos takes the Emeralds in the past is because the island...is NOT an ISLAND, it is still part of the mainland.

Also, the Death Egg's weight is NOT why the island fell the first time, not alone. Since the Death Egg is a huge artificial satellite, the other factor is gravity. While falling and picking up speed, when the Death Egg hits, it hits with more of its normal weight. This amount could be calculated by applying all the G-Forces, weight and speed of the Death Egg when falling. Why the Island dose not start floating between the short moments between S3 and S&K is because the Master Emerald was holding the Island 'level' on impact, so it stands to reason it was doing so when Death Egg took off for that moment. It was holding the Islands position according to height. Since it was not being 'commanded' to raise the Island, why would it do so?

By the way, it is mentioned that debug allows Knuckle to get to Sonic Sky Sanctuary and Death Egg. However using Debug on Death Egg to explore the entire level... at some point there is a drop (that WILL kill you), down there is a one way door, and you are on the wrong side. Debug to go through and follow the path. It is a dead end. However there are Knuckles elements here (like rings set in groups for Knuckles to grab during a glide (like in the second zone)). So it's clear he was originally meant to come here in early versions of the game.