It was never stated in the show, but I thought the center of the triluminary looked more like a computer chip than a stone.
Someone told me that it was supposed to be part of Sinclair's link (which would have gone back in time with him if he had continued as the main character of the show). Notice how they made sure to mention OVER and OVER again about how the links don't use adhesive, but are DNA coded to the wearer. The reason that it reacted to Sinclair is that it was coded to respond to his DNA. It reacted to Delenn because she is one of Sinclair/Valen's descendents and contained enough of his DNA to activate the chip. It also would have kept someone who was not "the One" from activating the Chrysalis device since the key component (triluminary) only worked for certain people.
This is the answer I have heard before and it does make the most sense to me. That explains why it reacted to Sinclair when they were interrorgating him, and why it also reacted to a "decendent" of his.
It doesnt explain how all 3 were in Episilon 3 though. What MAY have happened was this:
1) You will note that Sinclair did not have his link with him in WWE --- he was an ambassador to Minbar at that point. He even commented when Sheridans link went off. His link may have been somewhere on Minbar. Remember from the book "To Dream in the City of Sorrows" Sinclair stayed in Valens old house while he was there with the Rangers.
2) Its possible that as time was drawing near, Minbari who were "in the know" took Sinclairs link while he was on Minbar working with the Rangers. Perhaps they simply took it, perhaps they replaced it with a look-alike so he wouldnt notice it was missing. He probably didnt USE it anymore anyway, maybe it was just a keep sake at that point so why would he notice it wasnt the same one.
3) The Minbari who may have taken it was instructed to do so by Draal and it was taken to Episilon 3 where they made 3 Trilumanaries from it.
4) A year later, in WWE, those 3 trilumanaries were sent back with B4 and Sinclair/Valen.
5) They were then kept with the Minbari as mentioned above over the next 1000 years.
One thing to note: While this seems confusing, as described above there are NOT more than 3 Trilumanaries (except for brief overlap period).
They arrive 1000 years in the past. There are just 3.
They are kept up until Sinclair goes to Minbar. Still 3.
Link taken to Episilon 3 and 3 are made. NOW there are 6.
The three that were made are now taken to the past in WWE. The 3 from 1000 years ago still are in the present.
Damn its like trying to figure out about 75% of the Trek plots.
Anyway, that is what makes the most sense to me. Anyone agree? I dont think its ever been outright stated what they were or how they were made, but this seems to fit so its probably as good an answer as can be made.