Hi Cordey,
I took a look at the footage you linked and the issue you are seeing is certainly an odd one. Just looking at the footage it is difficult to say what the exact cause may be. Since you can see it when you playback the footage on the camera itself that indicates it is being caused by something in the equipment.
It would be good to check if this is related to stabilization. If you are using digital stabilization the camera misreading positioning could cause issues like this, or the physical stabilization could cause issues like this if an element moves incorrectly.
If you are using digital stabilization it would be good to try turning it off, shoot some test footage, and check to see if the same thing happens. To check the digital stabilization setting have the camera in movie mode, go into the Menu, go to the seventh page under the red camera icon, select IS (Image Stabilizer) Mode, on the next page select Digital IS, and set it to Off.
If the same thing happens with the digital stabilization turned off the next thing would be to try disabling the physical stabilization system. That can be done by flipping the IS switch on the lens to Off. That would disable both the lens IS and the camera in body stabilization. Once you've done that shoot some more test footage to see if the same thing happens.
