Hi, did some further research after I again experienced shut down in vicinity of another airport. It again had to do with add-on scenery, The reason was that one of the add-on airports close by called for changing the AP file in the Scenery/EURW. Unfortunately this changed few other airports in the vicinity and probably did not agree with the SRTM BGLs I had previously installed for this region and also some non airport scenery I had installed close by. The altitudes were probably confusing and FS could not deal with it. Removing this add-on airport and changing the Scenery/EURW airport file back to the default AP951140.BGL fixed the problem.
Also on initially mentioned Linate shut downs. I have actually noticed that I had two AP files (EFCADs) activated for LIMC airport causing the shut downs (previously thought it is the trees in airport vicinity, but not so). One EFCAD came with the add-on LIMC and second God knows from where. Removing one EFCAD fixed the problem. Smooth flights to Linate now.
I summary I think that these shut downs are mainly due to conflicting BGLs and probably not due to too much autogen, clouds or AI. Mainly if you have a strong Video Card which can handle these.