Hi Laurent.
No one has been given the definative answer to datastream priority for FSX terrain.
FSX was designed to have all your vector terrain elements in the same BGL... not spread over 2-20 separate BGL files. FSX was also designed to use the new vector BGLs... the backwards compatibility for FS9 elements was a very late addition... so AVOID LWM and VTP!
So here's what I would recommend: combine your shapefiles into their types ( FLX, EXX, etc ). Then place them in the same directory and let shp2vec sort it out. That is how MS did it, and that is how it should work. ( And use -addtocells for all your compilations, unless you are replacing an entire default FSX file ).
This way of working is quite contrary to FS9, where several BGLs and even folders were necessary. Then we just had to name them properly, and all was well.
You may need to search a bit for a program that will combine shapefiles for you, but it must be done.
Having 6 different flatten and exclude BGLs is not the preferred way of doing things for FSX, and probably will lead to priority issues just like you are experiencing. There is no "guru" to sort these out, because the Aces team has given us a tool to combine and sort the vectors in shp2vec... we just need to conform to their style by combining all our flattens into a single FLX shapefile (* for example ).
To make a long post short, all your terrain additions need to be in a single BGL, compiled with -addtocells option, in order to assure the correct priority of elements.
EDITED--
Hi Laurent.
It's occured to me that I may not be telling you anything you didn't already know, and may be just adding to your frustration. At this point, I think you'd need to include your source data, and decribe what you expect from it, in order to sort out the problem. SHP2VEC has worked for me as expected, and I'm a bit surprised you are having problems.
Dick