What Kanook says.
If it is "gummy" when you drain it and sticks all thick and nasty,to your finger when you feel in the drain hole and swipe around, it is probably like that on the whole inside and gears too. In that case, I would consider doing an additional change to flush it out. Some folks have used a cheaper trans oil for this as long as it will really be just for a flush and after a few hours go back with the sudt 2 and more new filters. It is your call though.. If it is just a little milky, one change might do it.
I'd check that rubber breather and filler pipe and make sure water isn't getting in there..wondering about the dip stick not seating also.
If it is a tractor, there may be hoses/pipes to drain all the bad transmission oil as well.. We had to do that with our 7420 JD... It had gotten water in it through a loose filler cap. collie