Hi Sargent;
Yes I can confirm an issue with our firmware that causes some "lag" on the Player 4 LED when you first power up your controller. I should just release that fix already, I've had it for almost two months but I was working on some other back-end performance enhancements and was trying to get them all released at once but it will probably be better if I just plan on two firmware update releases.
If LED colors don't seem to match up, they can try re-adjusting the position of that flexible rainbow LED add-on board at the shop. The stock Microsoft LED's are "0603" size and the clear plastic LED tube is designed for those Microsoft LED's, our Rainbow LED's I think at a "1210" size (a little bigger than 0603" so they need to be positioned more accurately to point up the clear plastic tube. What is happening is each of our player LED's has a little red, a little blue, and a little green light inside of it. If our LED isn't centered in the clear plastic LED tube, you might not see one of those colors. The red-green-blue need to shine up the tube and mix together to make the colors, but if all the light from one of those colors isn't shining up the tube it might throw the color off by the time you see it.
Hope all this makes sense, in any case, open up a support ticket and put a link to this thread in your ticket. And stay tuned for a firmware update, it will be firmware v0.9.0.0 or newer when it released and will take care of that "LED lag".
