On my SL system there is a mds folder in /private/var/db/. It contains two folders; messages and system. /private/var/db/mds/system contains 4 files; mds.install.lock, mds.lock, mdsDirectory.db, and mdsObject.db.
You should check in there to see if you already have that mds folder. I don't know how or why you have one at the root level. Odds are you can delete it.
Here's a terminal command to look at all the files and folders in /private/var/db/mds/:
ls -lR /private/var/db/mds
Thanks for that quick answer. As it turns out, I do have another mds folder in /private/var/db/, with everything you mentioned inside!
I'm guessing that the one I have at root level is just a copy then? Does anyone know how it might have got there? Can I just erase it?
PS: To see the /private folder, an easier way than launching terminal is just to "Go to Folder" (from Go in Finder or Shift + Command + G) and then entering the path (/private/var/db/mds/system)