Check your effects mate.
Some of them are making AE go nuts. (for example Misfire:Dust ALWAYS does the same thing to me!)
Try to render your clip without any effect (un-check them all).
If it succeeds then you ‘ll know that there is a “guilty plugin”.
So start adding one and render.. then the next one.. etc
May be you will get lucky and find another one that creates hard times to AE. If you will then please share.
p.s. Dave, do you use vodka for your brewing?