My phone has been doing the same thing. Got mine on Friday morning (10/14) and noticed it the next morning. It was plugged in all night long (wall-plug, not USB), but when I woke up and first checked, it was down to about 96% or so. I unplugged it and plugged it back in and it went up to 100% (over several minutes).
I thought it might just be that the new phone needed to have its battery indicator calibrated, so I drained the battery down to the point where it shut itself off (which took most of the day as I used the phone normally until drained), and then plugged it in and left it plugged in overnight again. The next morning, it was at 100% while plugged in. BUT after I opened my podcasting app and began downloading podcasts, I noticed it dropping to 99% and then 98% after another minute or so. This is normal for un-plugged iPhone battery drain, but my phone was still plugged in and still showing the charging indicator.
I un-plugged, re-plugged and it went back up to 100%. I again drained the battery down (this time to only about 20% or so) before charging again. Long story short, this pattern persists. It will charge up to 100%, and then it seems to stop drawing power from the charger, even though the indicators show charging status.
This is my first iPhone, but my iPad 2 remains at 100% while plugged in, no matter how long, or what I do with it while it is plugged in. So this battery draining while plugged in for my iPhone 4S seemed odd to me. I've been waiting to see what others had to say about it, so here I am sharing my own experience.
I'm guessing it's a "feature" or perhaps unintended mistake in terms of how the 4S communicates with the charger, rather than anything specific to iOS 5. A co-worker of mine has an iPhone 4 running iOS 5 and I spoke to him about this. He keeps his iPhone 4 plugged in (via USB) most of the day and it never drops below 100% while plugged in.
I'm eager to hear what other 4S owners have to say. Is this a "feature", software glitch, or hardware issue?
Message was edited by: ascii-T - type-o correction