I've been playing around in the Mediterranean recently and decided to give Malta one more try. At first I didn't get anywhere.
I tried all the suggestions in the posts above, combining the folders, using the files from the Pedestal campaign pack, nothing worked.
The problem is that the CTD doesn't happen on starting a flight, like most of the time, but only later, and then not always...
When I select Free Flight and select the airfield at Hal Far, after starting the flight I go to outside view and "look" at the airplane from the right front the game almost always crashes.
I made a test mission, a fighter sweep with four Bf-109s heading from Gozo towards Valetta being intercepted by Hurricanes coming from the direction of the airfields when near Valetta.
After a few minutes of dogfight I get the CTD every time.
It is not the airplanes, I tried several different ones, and it is not the GSL, I tried the new one, the original and none at all, no difference.
In the end I found out that it must be the "ValettaNEW" BGL file in the BSK Malta V2 Scenery folder.
Removing this file of course makes the Valetta scenery disappear, but without it the mission and also the Free Flight experiment work every time.
Unfortunately I don't know anything about how those files work, so I can't repair it, but at lest now I have a workaround which at lest enables me to use the rest of the scenery and the airfields there.