I've searched and come across many threads but nothing seems to quite match my issue.

When opening the liftgate inside, outside or from FOB it opens fine.
It will however refuse to close no matter how you try. You have to manually push it down. And even then it's pretty tough to get down. If you press the red button or the button in the vehicle you hear the motor try, and beeping it just doesn't go down. I'm thinking it's not the struts since it lifts up no problem to 90% of it's appropriate height.

Any suggestions? I haven't checked the fluid in the pump yet.

 

The rear hatch on this truck is the most temperamental one I've come across. My Lexus & Bimmer for example close at feather-touch of the hatch button or key fob button. On this truck I have to push the red button multiple times and sometimes give up and just close it manually. Using the key fob button makes no difference - sometimes it closes on first trial, sometimes it will not close after a dozen button pushes. The lock actuator makes a clicking sound with each button push (red button, key fob button, or driver side button, it doesn't matter). I am also sure my struts are fine because I replaced them and also replaced the lock actuator which was actually bad. This is what I too have read over time:

1. It works better when car has been started to charge the battery and battery voltage is high
2. Key needs to outside and near the hatch for it to close
3. You need to push and hold the button for two to five seconds for it work
4. Lift struts are worn (I replaced mine because the ball joint looked worn but the behavior hasn't really been different)
5. The lock actuator is faulty (mine isn't, I'm sure)
6. The lift pump is bad, water logged, or out of hydraulic fluid. Mine opens 100% of the time with the push of any button or lever and when I inspected the pump it was in pristine condition with ample amount of fluid.

Each of the above at one point seemed like the culprit. For instance I closed and opened it multiple times in succession after replacing the lift struts so I thought that was it until the next day it wouldn't close; When I found out about needing to hold button down for a few seconds (compared to other vehicles that work with one quick push) it seemed to have worked multiple times in succession, but then the next time it was back to it old self.

There is really no rhyme or rhythm to what makes the hatch close automatically. I've all but given up on this until your post. Let's hope others will chime in if there is a secret to pressing a button to close a hatch.
BTW: Mine doesn't beep until it actually starts to close so perhaps you symptom is a little different. The latch actuator makes a closing or opening sound with each successful/unsuccessful button press but does not actually beep until it is closing.

 

Go take a look in the right rear d-pillar. If your subwoofer is covered in yellow hyd fluid, the closing circuit probably has a leak - it'll typically drip off the headliner and down onto the woofer and the electrical connections around it.
The hyd pump (located in the deep well under the spare tire) has two circuits, so it can open normally or close normally, depending upon which circuit is intact.
So you have a leak in the closing circuit.

One of mine does this what yours is doing; as well as open slowly and not completely. I hear the pump, and all the requisite bings.

All that really means for me is that I have to close it manually. With no fluid in the closing circuit, it works just like a normal tailgate.

 

Thanks guys. I'm going to look into Max's suggestion. I'm pretty sure I don't meet tadi's suggestion with the exception of number 6. Worse case like you said Max opening automatically with my hands full is more important than manually closing.

 

if you’re lucky the leak is down in the well by the pump and you can fix that easy

if you’re like me it leaks from the actuator, which necessitates removing the interior panels, headliner and perhaps the side curtain airbags - all of the above is a major hassle.

 

I'll check the pump. Not worth the hassle of ripping down liner. Thank you!