Just an update - After hours of debugging the only thing I've been able to conclude is that the cart session is dropped (not just single items) randomly when there is more than one item in the cart.
My original diagnosis wasn't totally right as this appears to happen randomly throughout the site regardless of category. The session objects appear to be normal up until the random moment, then it just disappears. Thats where the debugging runs into a wall.
At this point I'm sure its the cart, but still not sure how to get to the root of the problem.
Any input at all wold be appreciated.