I will have to defer to Dave then, as I'm not sure what it might be, make sure you are also using the latest version of makerunways too, I think its version 4.41.
It sounds as if something has gone amiss during the makerwys process. If you open the file name PFE_FS?_Gates.dat and search for EHAM you should find an entry for all the gates. if you can't find EHAM we will have to look at the Runways file and try to see why MakeRwys did not extract the data. It may well be the Aerosoft files have done something a little different that normal.... but I'm only guessing