Sometimes fsck shows that a filesystem has no errors, but in reality it has. I had a similar issue once, and if you want to check that filesystem, you have to use force. I'm not sure what type of a filesystem you're using, but let's assume it's ext4:
Emergency help:
-p Automatic repair (no questions)
-n Make no changes to the filesystem
-y Assume "yes" to all questions
-c Check for bad blocks and add them to the badblock list
-f Force checking even if filesystem is marked clean
-v Be verbose
-b superblock Use alternative superblock
-B blocksize Force blocksize when looking for superblock
-j external_journal Set location of the external journal
-l bad_blocks_file Add to badblocks list
-L bad_blocks_file Set badblocks list
So, the line you need is:
# fsck.ext4 -pvf /dev/sda1