I had the same issue. Also with my titlebar's battery metter NOT there but appearing 1/3rd the way down the screen when the PHONE app came on. I simply disabled "show titlebar clock" in the HHC appy, soft reset and viola! The battery meter is back up on the titlebar and the PHONE app popping up has stopped. Interestingly, I noticed the title bar time DOES still show up in my apps (which is fine for me) albeit not when the TODAY screen is up which is also good because I have the HTC time staring at me right there. I just discovered why: the "Display the clock on the title bar in all programs" option in Settings/Clock & Alerms/More Tab is CHECKED (Selected, or "on"). So I would reckon that if you UN-checked this as well the title bar would be 100% gone. However, I'm leaving it checked (while in the HHC it's disabled) because I like how it's set up now.
