Tazman, thanks for the information. - I have the Seido 3500 Mah battery too with the same problems described above. I have since root my phone, and once you have done that you can download the Battery Calibrate application from the Play Store. I've used it a couple of times but it didn't fix my problem. I'm going to run through method #2 since it's from HTC and get back with an update.
In summary, I like most people with EVOs want to have a charged phone before leaving the house, so you probably stick it on the charger when you get home regardless of the charge remaining on the battery. I'm assuming this causes some bad cells over time like the older batteries use to do. Nonetheless, something I found intriging as I proceed through the steps, after 100% charge, and power down and charge for an hour, the phone was 80%. This tells me the calibration must be off. Ill keep you and everyone posted as I complete the steps.