I'm really lost. I'm running ADE v1.20 and I'm having the same runway altitude problem, but that's just the start of it.
I can't figure out how to flatten terrain with ADE (is it possible? jojlino's post seems to indicate it is), so I flattened it with SBuilder and then built my airport over the same area in ADE, but my runways are at 0 altitude.
I tried to do the XML work-around, but I can't find the "exoprt to xml" option in the settings/option/general tab.
The only tick-boxes I have in that tab are "locking disables editing", "auto-set parking and and apron link surfaces", include approaches" and then "normal", "detail", and "full" under the "logging level" heading.
Am I missing something? I've been fighting with this all day and my brain is starting to hurt.
Thanks in advance for any advice!
BTW. ADE is a great tool. I never thought it would be so easy to build a whole functioning airport for FSX! Bravo!