This happened to me very recently.with EHAM.
PFE hadn't for some reason added Aerosofts Mega Amsterdam runways to it's database even though it was upto date in Runways file and in FS2004...but was correct in FSX and PFE....figure that one out
Anyway, i uninstalled Amsterdam from FS2004 and my system,reinstalled it,ran makerwys and rebuild PFE database in FS2004 and now all is up to date in PFE.
So i'm thinking maybe some scenery has to be higher up in the library to work correctly above any landclass thats in there!