The only thing you can be sure of, is that you DO NOT have to remove KFLL. We already checked if there was any problem with it and, right now, there are only 2 users reporting this crash, which should be otherwise very easy to notice. Of course, assuming you are using the AFCAD that comes with KFLL (current 1.2 version), and it hasn't been modified.
Yes, a duplicated AFCAD might create a problem, especially if you don't keep KFLL on top of it on the Scenery Library. There is a reason why the installer put it at the very top.
To look for duplicate AFCAD, you can use the free FSX Airport Scanner, which is made by the same people of ADE. This will check how many AFCADs you have for a specific airport. You should have two, and only two, at maximum. The default one, which is named something like APxxxxx.BGL, and it resides in the NAME scenery folder, and the one we supply with KFLL, which is named AP_KFLL.BGL, and it's located in the fsdreamteam\KFLL folder.
If you have more, delete all the extra.