I have noticed something similar on my EA41, especially at the lower modes (I like to use the 40 lumen mode to light up the room while I am up at night). After I have been using them for a while the blue led will start slow blinking while the light is on, but I will still get 3 blinks when I do a battery test. Later on, I will be getting an 'I'm dying here' blinker, yet still get 2 blinks on the battery check. But I know I will soon have to recharge at that point.
I went back and looked at some of the dv/dT curves our faithful reviewers have published, and noticed something interesting. On almost all the curves, but especially at low current drains, from the time the cell drops down from its initial voltage until it hits the knee and starts to dive, the voltage measured will only drop by about 0.05 volts. I'm guessing for the rest of this, but I think that the blinker is running off of a dv/dT comparator, and that further, because of the steepness of the curve after the voltage starts to seriously drop, the dT time interval is not very long. That would mean that when the cell is first starting into its final voltage drop dv will change enough to trigger the warning, even if the drop is not that substantial yet. Then with continued use the dv value starts to increase more rapidly as the cell moves down the curve, triggering more urgent warnings, even if the actual voltage may have only changed by 0.1 or 0.2. Of course, this is all (hopefully) intelligent speculation on my part, and I hope one of our resident battery gurus will correct me if I am wrong.