From what I understand, it will always recharge the battery to 100%, but only if when you plug it in, the remaining charge is below 95%. Try it, you'll see: use it on battery power for a few minutes, let it drop 2% and plug it back in. The magsafe won't bother making up for those 2%.
As far as the amber light still on at 99%' I've noticed that this last 1% can sometimes take a long while to charge. At one point, mine will go from green to orange every two seconds (with readings oscillating between 99 and 100 at the same frequency) for a couple hours. Tiny glitch, but it doesn't affect performance or stability in any way.
cheers