I'm sorry I cannot help you, but I've always wondered, if this happens, can you manually lift the top back up to cover the interior? or is it pretty much stuck down?
I think it means you're out of hydraulic fluid. Take the rear seat out and there should be a plug on the motor somewhere, take it out and make sure there's fluid in it.
You may have a hydraulic leak and some air has entered the lines. I'm assuming it requires less force to lower the top than to raise it, which may not be true.
I suggest you try this test:
If you can, raise the top manually, but don't latch it to the header.
Next, see if you can still open it with the switch just 1/4 to 1/3 of the way; now it should be a lot easier to close.
Finally, see if the switch and hydraulic system will close it from there.
If yes, I would say the mechanism is weak (air in system, fluid leak, bad pump) or something is binding mechanically when it is fully lowered.
If no, it sounds like a bad pump (even though it is running, it may not be pumping fluid into the cylinders in both directions).