Water in gearbox

When you drained the gearbox, did you also drain the ring gear compartment? The plug for this is another hex socket head plug located near the rear end of the housing on the centerline of the transmission between the drains for the clutch/ brake compartment. As the transmission and the ring gear share the same oil (they're connected internally) there might still have been some water/oil mix in there. I would have thought the hydraulic oil flush would have taken care of the water but if the ring gear still had some in it, that's about the only place it could have come from. The only other reason I can think of was the tractor not being level and may have been facing uphill a bit.
The leaky radiator and water pump should have no effect on the transmission.

[quote="Betch"]Filled her up with nice fresh gear oil and gave it a run a week later. Now the strange thing is when I checked the oil again it is all white and milky again. It has not rained so where could the water be coming from?

Any ideas becouse I have none.[/quote]

you might have 'milky sludge' coating the insides of the gearbox,clinging to the walls of the box.When you drained the box initially,you got the bulk of it but the gearbox still had moisture and sludge which now contaminated the new oil..drain and flush with kero or diesel twice or three times,then refill and run with your gearoil.Sometimes the contaminated lube will turn to paste inside,and it's tough to purge it.Stinks to high heaven too!