I have that problem on my 2002 sometimes. For my car, its a two person fix but not manual. One person has to stand by the trunk while the other pushes the close button. Then, when the trunk opens to allow the top to come up, i give that little black thing with mini wings a gentle tug up and it closes nicely.
Also, i turn the key on and off to reboot the cycle for closing the and opening the top. The only times i have had problems is when I stop in middle of the closing or opening process. It appear to dislike interruptions.