Repair disk on Snow Leopard using a bootable USB, in order to upgrade to Lion
Using an installer image that is bootable, whether DVD or USB or simply an external partition, is always a good idea when repairing disc problems, because it allows the partition you need to check to be fully unused for the duration of the check.  Otherwise it's trying to fix itself, whilst running the OS and the fix actions at the same time.  So feel free to use whatever media you have to initiate a repair, the Disk Utility program is available in any OS X install media, just boot from it and select from the menu.