This doesn't have anything to do with JFK.
You simply exhausted your avaiable RAM. Obviously, since you have installed a LOT of addon for a specific are, the problem might have happened with any of them. If you already were on the *borderline* of exhausting your memory without JFK, you can't expect adding it would improve it.
But it would have happened just the same if you already have JFK installed, and added all the other addons after it. You might have had the impression that the *other* addons caused the issue, because it would have manifested only after you installed them.
So, it's not anyone's fault, it's just the combination of so many products in such a small area, that simply doesn't fit in your memory. Also, you are not saying which airplane are you using. I bet it happens more frequently with PMDG 744, which takes about 800 MB of RAM alone.
The issue is, regardless of how much system RAM you have, FS9 by default would never allocate more than 2GB, unless you modify BOTH the FS9.EXE to enable >2GB or RAM AND you modify your Windows startup with the /3G switch to allow for this.
To do this, have a look here:http://www.simviation.com/cgi-bin/yabb2/YaBB.pl?num=1199566076/1#1