Now why is that... Seriously
16 GB is not really 16 GB anyway. In reality it is 14.9 GB
Thats because Hardware manufacturers see 16 GB as 1000 MB, which is 1000 KB, which is 1000 B
When reality, 16 GB is 1024 MB, which is 1024 KB, which is 1024 B
So take your 16 GB and x1000x1000x1000, /1000/1000/1000 = 14.9 GB (which is usually how software would show your space.
Then when you take into account the nearly 2GB for /system 1GB for /cache and the various other little partitions, this leaves the GT-i9300 with 11.25 - 11.35 GB free.
Now, some US versions show the /system and /cache as part of that space. I'm not sure why. Probably to stop people calling carriers and asking "wheres my space?"
In regards to the OP, I would recommend making a nandroid backup, backup your sd card to pc and do a factory reset including wipe data of sd card.
Then restore the minimum data back and do a nandroid restore. It looks like a problem with the file system