Are you running Lion (10.7.4, as your profile indicates) or Mountain Lion?
Regardless, if you let your battery completely drain, it can take up to 2.5 hours or more to fully recharge (if you've an ongoing download, you should be connected to mains and should set your Energy Saver preferences to Sleep>Never). I would just monitor the battery and make sure that it gets to a fully charged state. You may even want to download and run coconutBattery to monitor exactly what's going on with your battery.
As to why you're CPU is bumping to 100%, I don't know. If you sort your processes by CPU % in Activity Monitor, do you see one or more 'runaway' processes? If so, try to quit those processes.