I bought my 3G used and it had the same problem. The first day I used it, I made sure it was charging all night. Took it out, and used it sparingly, as I have heard of the battery issues accompanying the 3G. It showed full all the way until I got home. I was tickled to see the battery last all day and still be full, or close to it.
Then it happened. I was going to check my email as I sat down to my desk. I pressed the home button, the slide to unlock screen showed up and I slid the slider. Then, blink, and off it went. I thought...OH CRUD!!!!......I just bought a brick. I then went through some steps I read on this forum of trying to reset the phone, plugging it into the computer, etc. Nothing. I was biting my nails and pulling out whatever hair I have left.
Then I tried my last ditch effort of plugging it into the wall and see what happens. AHA!!!!!, life. But the battery meter on the screen was showing a small sliver of red and a little lightning bolt showing that it was charging. The battery was completely drained, and I never knew it.
I had upgraded the OS to 3.0 the previous night and thought that might be the culprit. I could not pinpoint the cause of why the battery meter was doing what it was doing, showing full when it was not.
Over the next few weeks, the battery meter slowly started to get in sync, and show a close exact of battery life left. I even downloaded a program called battery meter for free just to have a second opinion on the status.
I do believe that it has something to do with the circuit embedded in the battery that may not be interfacing properly with the iPhone OS, or maybe it just needs to be trained all over again after the OS upgrade.
I have not been able to duplicate this issue with my 2nd Generation iPod Touch that I upgraded to 3.0 on the day it dropped. So must be related to the phone portion of the device.