We have "resolved" this by migrating the server to an Ubuntu Server 14.04 install.
I am facing the same issue on Moodle 2.8.1 even though the server is running Ubuntu Server 14.04, does anyone have any idea about this issue?
Are you using Clam AV? I noticed an improvement in file upload speed after changing the path to use the clam daemon on Moodle 2.6, Ubuntu Server 14.04.
clam AV path: /usr/bin/clamdscan