So i discovered my server had ran out of inodes yet had lots of space left.
This caused quite a few problems for me!
After a quick search i found
find . -xdev -type f | cut -d "/" -f 2 | sort | uniq -c | sort -nat root showed me where the inodes were being used.
A little deeper investigation i discovered this post on cpanel’s forums
http://forums.cpanel.net/f5/strange-directory-inside-root-270191.html
so with the cpanel script
/usr/local/cpanel/bin/purge_dead_comet_files I could purge the old comet files and release all those inodes again! I had previously been under attack from spam email.