I have had this problem really badly on my 99 also.
I also was able to solve it by putting a little pressure on the bottom of the door while lifting the hatch latch. Worked every time.
Just recently that quit working for me and I was going to just replace the entire latch mech. (because I have a spare), I had a feeling that the screws were not going to give up with out a fight, so I lubed the daylights out of everything and for some reason, this time it fixed the problem.
I think my problem was the handle converts the vertical motion into horizontal motion, I haven't seen how this works exactly, but I think that part was building up too much resistance and failing.
So.. yeah.. I don't know what the problem was, I just know that a ton of WD-40 solved my problem beautifully.