Anyone ever consider that a transporter disentigrates you and creates an identical copy of you at the destination? Technically anyone who has ever used a transporter is dead...replaced by a line of clones...if it wasnt so, then how do you explain Thomas Riker?
I think the concept of Thomas Riker was the BIG mistake, where the transporter is concerned.
The original idea that I'd seen most people claim how the transporter works is that your entire molecular pattern is scanned and then very rapidly disassembled, beamed to the target location, and reassembled. So, all of your "bits" are sent to the destination--no "killing and copying" going on (otherwise how could Barclay have his "transporter psychosis" bits, partially aware during the beaming?). That's why all of your clothes and equipment goes too. If not... then "local matter" would have to be sucked up and assembled into the destination beam to compromise you and all of your gear. That doesn't make sense.
So... with Thomas Riker, a duplicate is created.... FROM WHAT?? The matter to compose his body had to come from somewhere. And if transporting means there's just one copy of matter being sent... then either Riker would have reassembled back on the planet or back on the ship, or... two of him assembled each from 50% of his original matter (translucent Riker?).
Thus, I just pass off "Pegasus" as a mistake in the series. They do happen, contradictions that can't be easily explained away without major fan wanking. You just have to take it as an error and move on.
The extra matter probably comes from the measurement the transporter crew took, to reestablish the quantum-state matrix of Riker.
While the planets conditions were the reason there were two energy-matrices at two destination(most likely with 50% content each), the transporter crew probably boosted the recieved signal (to compensate for the lost energy of the matrix)over the point to were each matrices had enough coherence(because there would either be two stable matrices or none) and filled in the lost information (reconstructing algorythms). They now created two intact patterns at two destinations.