I tested the afcad, and it works perfectly without any runway/taxiways disappearing, however I have three notes.
First note is that there are a few problems in your taxiways. Not big problems, it can be fixed easily by just moving the blue circles of the taxiway.
Your Afcad
The fix...
Second note was that the afcad does not look like the real airport, maybe its the old layout but its surely not the new as seen on this satellite image from
YAHOO.
Last but not least, I want to remind you that you need to do a EXCLUSION box for the airport so it can delete all building, trees, and autogen above your airport. Look at this picture to understand what I mean.
As you can see, the default airport buildings is above the taxiway
Great work so far, keep it up!