/proc isn't a normal filesystem so those sorts of errors are normal (it most likely means that those processes are no longer running). The -x option will prevent du trying to read through proc.
The way I tackle this sort of thing is to do
Code:
du -xSb / | sort -n
Which will present you with a list of directories and the size in bytes of their contents (not including subdirectories which will have their own entries), from smallest to largest. Then you can just scroll back through the list and find ones which seem to look bigger than they should be..
It won't find the culprit every time as open files may not show up in a du scan, but it's a good starting point.