The whole issue behind bump charging is not as big of a problem as it is made out to be. The reason the battery drops so quickly without bump charging is the battery charge trickle effect and it is intentional. If you charged your battery to capacity over night and it didn't trickle down then it would be constantly charging even when full. This would cause a shorter life of the battery in the long term. By constantly bump charging your battery you are decreasing the lifetime of your battery as well.
From what I have read, every so often (1 or 2 times a month) you should ruin your battery down to 5-10%, then fully charge it and bump charge it. This seems to recalibrate your battery readings.
I have posted this in another thread but this will help you understand that bump charging is not good for your battery:
I really think HTC should release a fix for this. The fact that we have to either turn the phone off, or go through this entire bump charge rigmarole, means there's a problem. It's my one gripe with this phone.
Ever since I rooted, and started using SetCPU I make it from 6 am till 10:30 at night on a single charge. No joke. I don't use my phone a lot at work, but I get a TERRIBLE signal in the cinderblock building I work in so that eats some juice during the day. In the afternoon/evening I am always playing with the phone (words with friends, web surfing, angrybirds, etc) and it dies before 11. I usually run the battery down to 5% -10% before powering down and charging it. No more bump charging, just charge with the power off.
Are you saying this is an issue with the processor in the Incredible?