The top opens fine and sits down in the well properly, but when the rear deck lid lowers into the fully closed position (where it is flush w/the body panels), it will not latch. It will hold in the closed position for about 3-4 seconds and then raise up about an inch or so.

 

The latch for that is visible with the tonneau cover raised.
Examine it for any obvious problems, lube it up good with lithium grease and inspect the 2 hydraulic lines for signs of leakage.

You can latch the rear bow manually by using a 6 mm hex wrench on the latch when the trunk is open.
Press the rear bow down while turning the hex wrench, I don't remember which way, but pizzaguy ( Mark ) has a video on here you can search form he states which way latches.

 

Rear bow latching is not the problem.

When the top is in the stowed position, the rear deck lid will not latch in the closed position (top is down, properly stowed in the storage compartment). I think you are addressing that issue in your 1st comment regarding lube and hydraulic inspection.

 

OK, sorry.
Same applies to that latch, other than you use the special tool ( or thin 10 mm open end ) to manually operate it.

 

Here is a picture of the tonneau cover latch:



Indeed, it is the one that gets locked with the open 10-mm wrench if needed. See pizzaguy's video: https://www.crossfireforum.org/forum...operation.html

Is there an obstruction in the storage well, that doesn't allow the top to fold down completely and thus the catch on the storage cover (tonneau cover) doesn't quite make it far enough into the latch?

If there is a lot of dirt in the latch, then the mechanism may be sticky that indicates the catch from the tonneau cover has arrived. Basically, the hydraulic cylinder in the latch is pressurized before the cover is all the way down, but the cylinder cannot close the latch before the catch from the tonneau cover has pushed a mechanical trigger inside the latch, and that trigger could be a bit jammed from a bunch of dirt...

Klaus

www.tophydraulicsinc.com