Ok, here is what I see. The battery indicator is wrong and yes, it does lose charge while plugged in especially over long periods of time.
Using the HTC Battery Widget - I noticed that the Voltage gets to about 4211 mV when fully charged at 100%. However, if I leave the phone plugged in all night and wake up to a 100% charged green led phone -- I'll notice that the Widget says my Voltage is 3800 mV and very quickly after unplugging I'll go to 90% within a few minutes.
Using the bump charge and watching the voltage, I can make sure it gets to 4200+ mV and thus retain 100% charge longer, but seems to me to be kind of pointless especially when I leave for work immediately after I wake up in the mornings.
Another observation: If I unplug the phone, and use it for a bit, get it to 90% battery life, I'll see that the Voltage is 3800 mV, plug it in, and it will get to 4197 mV pretty quickly, but over the next hour, the % will go from 90-100% even though the voltage stays around 4190~ mV.
This seems to me to be a pretty serious flaw in the way HTC charges their batteries. But at least now I know what's going on. Maybe this helps battery life instead of constantly charging/uncharging/charging to keep a phone at 100% while it is plugged in? At least that's what I've read.