If it was shut down incorrectly then boot from the live cd, enter a terminal and run
From this you should be able to determine the device address of your linux partition if you don't already know it. The clue is to look for the word 'Linux' at the end of the line and then look at the address at the beginning of the line. It will probably be something like "/dev/sda2". Once you have determined this run
substituting /dev/sda2 for whatever the correct address is. This will repair the file system for you. When this is complete remove the live cd, reboot and see if that has fixed it.