Buffering Issues since a few days ago

A few days ago all media on the server started to constantly buffer once every 15-45 seconds when played from a remote network, this does not happen on the same LAN as the Plex server. This happens on all remote networks that have been tested (at least 8), so it's not an internet issue on the remote network side. And the server side has a full gig connection up/down that is rock solid.
It appears to be an issue with the transcoder, as when it buffers the transcoder seems to spike quite a bit. There had been no hardware or software changes to the server for weeks, when this started happening I upgraded to 1.2.5 and then 1.2.6 and that didn't solve the issue.
Hardware/Software Setup:
OS: Debian Wheezy
CPU: Xeon 1275 v2 3.5Ghz CPU
RAM:6gb
Running the release from this repo: http://shell.ninthgate.se/packages/debian/
All media and transcoding temp files are stored on a freenas storage array that is working just fine(very overpowered).
Running in a VM on it's own host for testing
Any ideas?
edit: added info.