FSDS's boolean is quirky at best.  It is being (slightly) improved for the coming update.

However, I would recommend that you try to do all your window cutouts at one operation .  Join all your different "tools" (make sure they don't overlap) into one "tool"  part, and then do the boolean operation.

Another thing you can do is split off the polygons that are going to be affected from the fuselage part and do the booleans separately.

Since in FSDS you "keep"  the original part, it's relatively easy to then join back teh booleaned parts back to the original.  That way you get a slightly cleaner mesh.