Root filesystem filling up, no big files

Here is what I use in trying to figure out problems like this.

du -s `ls -a | egrep -v '\.\.'` | sort -nr | head

It will show you the usage per directory/file in the current directory. From there you step down into sub dirs until you find something obvious.

Having everything in one big partition can make diagnosing problems like this difficult. Another approach to try is using

lsof 

to see what files are open by the various process and see if you can find some clues. This is very hit or miss though.

It sounds a lot like a similar issue I have all the time with deleted files (but the reference is still there).

If we're talking a Linux system, run:

lsof +L1

This will be a list of deletes files, but are still open and being used by something. The key is to get whatever has the filehandle open to release it.