This has happened to me, too. The problem I experienced relates to the MS Wireless Controller I purchased, not the one that was included with my Premium system. The controller that was included with my Premium system works fine with AA batteries and the Rechargeable Battery Pack. The controller I purchased seperately works fine with AA batteries, but I have a similar problem to what you are experiencing when I use the Rechareable Battery Pack. Most of the time, when I Turn the System Off with this wiress controller, the #1 area will be dim green. However, there have been several times when both #1 and #2 would be dim green, which mean the entire upper half was dimly lit. MS told me the exact same thing; they said that this would not perfect game performance in any way. MS said that if I had a problem with this, then I could take the controller back to the store if it was still under warranty.
Here is one thing that MS did let me know: If you push the Start button while the light is dimly lit green, then the light will go out the way it is supposed to. I pushed the Start button, but the light only stayed out for about 5 minutes. However, I let the light stay on for a few hours, and then I pushed start, and it didn't come back on. I currently theorize that if you turn the system off, and then wait 5 seconds to push Start, then in 5 seconds, the green light will come back on. If you wait 10 seconds to push Start, then the light will go out, but only for 10 seconds. And if you wait 3 hours, then it will take the light at least 3 hours to come back on. However, I also theorize that there may be a certain time lengh border, such as maybe 30 minutes, where if you press the Start button, then the light will stay out for good. I haven't done all of the detailed testing that you have...but here are some theories for you to work with. Anyways, the Start button is a factor you might want to consider.