I didn't see anywhere where someone has stated this, but I've probably missed it.. I think the simple explanation is that the phone doesn't seem to be doing a proper trickle charge. Take the following picture for example:
The black vertical line is where I took the phone off the charger. The blue line is the battery percentage, and the red line is the battery voltage. Notice that the battery voltage had been dropping slowly for probably 1-2 hours before I took the phone off the charger. In this case, the phone was left at 93% after unplugging.
I've seen this happen before, but the last time I saw it was when I noticed the red light was on when I woke up, indicating charging. What happened was that the voltage had dropped down a bit and charging had came back on, so the red voltage line dropped similar to above, but then the charger came back on and topped it off, causing the red line to slope back up to 100%. In that case, I was at 99% after unplugging.
So is it not trickle charging, perhaps? That's what it sounds like to me. I haven't looked at the battery.prc program during this time to see what the current shows (negative for discharging or positive for charging) but the graph from batterygraph indicates the phone is basically off the charger for a while. Note the slope of the voltage doesn't change at all.