Hi Zoran,
I'm not sure if you have both versions installed (Steam and boxed), but for myself (Steam only) the SCENERY.CFG is located and updated in the C:\ProgramData folder, NOT where FSX is installed.
I know the SCENERY.CFG is also located in the FSX installation folders, but the one actually used by FSX is in the ProgramData location.
I hope this helps!
Stevan
EDIT - this was also true with my original FSX boxed version.