This is an old thread, but it never had resolution...I had the same issue, and solved it with the help of this thread so I figure I will chime in.
New to me John Deere 790, exact same problem and symptoms as original poster. I have never owned a tractor before and don't really know hydraulics, so I searched around to first figure out if I had a problem, then how to solve it.
In Short, my male quick connector to the loader for the retract/down system of my loader had failed. A tiny retaining ring had popped out which then took pressure off the spring that pushed on the plunger that should have opened the valve on the female/tractor side of the quick connection. All looked normal from the outside. If I had a pressure gauge, it would have also shown all was well...
What made it confusing, same as OP is that the loader seemed to work. It had full power to lift and would go down when I asked it to. What I couldn't see is that it was only gravity pulling it down, not hydraulics.
I trouble-shot it by loosening a fitting at the lift cylinder and seeing if I could shoot oil out. I couldn't on the down, so I traced it back to the bad fitting.
Here is a picture of the pieces that were bad.
View attachment 382488
$12 later I can pull my front wheels off the ground at idle. Nice.