Boot up from your system installation disk by holding down the "C" key. Go to the second screen pull down menu to Utilities -> Disk Utility and repair the drive till it runs clear. If this ails do a reinstall of the system using the archive and install option. I suspect that your hard drive is starting to fail but will still work after it gets warm. If the drive is an old one I would select the "write zeros" option to map out any bad blocks. This takes a while but will eliminate future problems. This may only last for a short while, so I'd make sure my data was backed up and start looking for a replacement hard drive.