The transmission and rear end are separate reservoirs. The hydraulics draw fluid from the rear end. Many people check the transmission fluid level with the transmission dipstick, and think they"ve checked the rear end fluid level as well. Just in case this is your situation:
There are two small SQUARE HEADED fluid level check plugs on the right hand side of the trans and rear end.
As you are seated on the tractor, the transmission check plug is above your right toe.
The rear end check plug is behind your right heel. Difficult to see - you may have to squat down to see it.
These are small SQUARE HEADED pipe plugs. Pull them out and add fluid until it comes out of the hole.