My FS2k2 scenery is stock, so I've no 3rd-party scenery add-ons, but I rarely use this program so I'm not familiar with everything. How well, if at all, does everything line up when you select take-offs from these areas?

If it's a conflict with add-on scenery, you could make a new folder and move all but the stock bgl into it. If the problem persists, your stock bgl may be corrupt and you will have to reinstall. If the program works properly, however, you can reintroduce each bgl, testing each time, until it returns; then remove and omit the offending add-on(s).

"Stock" would be what was provided in the original program installation; i.e. what you started with. I'm not at my own computer at the moment (will be a quite few hours yet).

[EDIT]
Stock FS2k2 scenery .bgl files:
dem4km.bgl
dynlib.bgl
lclookup.bgl
magdec.bgl
regions.bgl
seasons.bgl
timezone.bgl
world.vis
worldlc.bgl
worldwc.bgl

Anything other than the listed stock .bgl files you have added since installation -- they are your add-on scenery files.

1. As said, make another folder (you can leave it named New Folder, Add-ons, Escrow or whatever you wish) as an escrow folder. Move all but the stock .bgl files into that folder. It is suggested that you also make a second "Stock bgl" folder; select your stock .bgl files, right click and 'copy', then paste the copies inside the "Stock bgl" folder.
    [note: Any add-ons (missions, locales, objects, etc.) dependant upon those scenery files will now be inoperative.
              It's best to fly stock aircraft, as well.]

2. Click on your fs2002.exe (or else start the program via your normal icon). If your stock .bgl files are not corrupt, you should be able to start a flight from or to any location that is included in the stock installation.
   [note: There are 40 stock cities (runways) available in Portugal besides Madeira (LPMA).
             GCFV, GCGM, GCHI, GCLA, GCLB, GCRR, GCTS, GCXO are the stock locations avaliable in the Canary Islands.]

3a. If the program doesn't work properly, it's probable that one or more of your stock .bgl files is/are corrupt and may need to be reinstalled.

3b. If the program works properly, then you can slowly move the add-on files out of the escrow folder a few at a time; with each file move, restart the program and make sure everything works properly. If the program stops working properly, remove the last added file(s) until the program works properly again: the file just removed is evidently causing a problem so leave it in your escrow folder. Continue until all files are out of the escrow folder except the problematic ones.