Sounds like the two frames are reversed or at least your second frame is the closed position instead of open? You'll need to switch them.
Be sure the door is positioned where you want it to be when closed. In JED select the door, hit enter, and check the frames in the thing editor. The first frame is where the door is when closed and the second frame is the open position. You'll need to edit these.
If you don't see "+thingflags", "numframes", "frame", and "frame" in the item editor then open the tool window (F9) and under Misc click "make door." These values should now show up. The values in the first "frame" should match the current x/y/z and pitch/yaw/roll numbers of where the door is now. Since you want your door to go DOWN then for the second frame you need all the numbers to stay the same EXCEPT for Z. To figure out the Z value, take the current Z value and subtract the height of the door. For example, standard 2x3 doors are 0.3 jku high, so subtract 0.3 from Z. Edit the third number in the second frame to the new Z value. [When you click on "Make Door" it will add to the Z value, assuming you want the door to go up.] Make sure the X and Y numbers are the same in both frames.
If you had already made the thing a door, to get the new values, in the thing editor window, click on "Copy as Frame", then paste this (ctrl-v) in the first frame. Then edit the second frame (change Z).
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Sylvicolus JK homepage
If I have ever made any valuable discoveries, it has been owing more to
patient observation than to any other reason. -Isaac Newton