Weird Battery Timing

Hey everyone, I have a MacBook Pro that I purchased about five months ago. Everything was fine until I downloaded Battery Update 1.2 At this point everytime I ran the machine with the battery I would receive incorrect times as to how much battery power was left. I would have a fully charged battery, and while pulling out the AC adapter it would state that I only have about 5 minutes left, and then it would put the message on screen that I'm running in low power mode, then the computer would shut off. I took my computer to the Genius Bar and had my battery replaced for a brand new one. I calibrated the battery but the timing issue still seems to be present. As I use my battery the time left fluctuates, it goes up and down. Before the update everything was nice and consistent. Any help would be much appreciated.
MacBook Pro   Mac OS X (10.4.9)  

Based on your description, it may suggest a conflict within permissions. You can verify permissions to see if your system identifies a conflict or otherwise perform the repair.
Repairing Permissions and/or Resetting the Power Management Unit (PMU) is known to resolve certain anomalies or conditions, and may help with your symptom. Neither process will compromise or harm anything with your Mac so it’s worth a shot.
Repair Permissions:
Go to: Applications/Utilities/Disk Utility
Select: your Hard Drive
Select: the First Aid tab
Select: Repair Permissions
Resetting the Power Management Unit (PMU)
If the computer is on, turn it off.
Disconnect the AC Adapter and remove the computer's battery.
Press and hold down the power button for 5 seconds and then release the button.
Reconnect the battery and AC Adapter.
Press the Power button to restart the computer.
Ref:
PMU: http://docs.info.apple.com/article.html?artnum=303319
User's Guide: page-95
Regards,

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