I've just run into bug 7257 and it seems there is a relation between that and this.

First, remove debris from uninstalled programmes using dpkg, as described in the wiki's clear up rootfs page. I suggest by name, rather than the automatic means, incase you remove something you later rely on.

Now for the bit I just found. Even if you don't have a UI file manager, you can still see what might be the problem, using good ol' microB:

1. Go to root directory and ensure you can see hidden files.
2. Look for files that really don't belong there.
3. Open terminal, and as 'root', rm the files you want to remove (for new users - copy & paste in the terminal needs to be done via the menu bar so you can take file names from the browser screen)

In my case, I found that get_iplayer had deposited a download in the /root folder so the whole system got clogged up.

If you can't decide whether something should be there or not, well, that's when to ask for help!