Possibly the gear syncro mesh is out of alinement with clutch I had avery interesting conversation with a gear box engineer he stated that if the gearbox is not set correctly the speed from the flywheel to gear box is miss matched.
Solution was to take it to a pro in gearbox to correctly set the syncro mesh on the gears and put it in correctly!
Its confusing to me as I've seen gearboxes like for like go right in, but apprently on some odd gearboxes they need setting up due to the miss match speeds?