I have found the reason...
Thanks drayotn for the clues, thank You Umberto for Your help.
The reason was VoxATC, or to be precise - their tool for correcting runways, which changed in RL since the FSX was introduced. They provide the tool, which corrects the airports, when runways have changed (Malta was on of these). I have disabled the scenery. Actually I totally forgot about this scenery.