I am having the same problem =LwS=Balapan had.
Vertical position is not saved after i release the zoom button and press it again (but snaps to there when i try to reposition vertical again).
Even changing it manualy at d3dx_user.ini doesn't help, it always show the default Y value (zero?).
And snaps to the correct one (which in d3dx_user.ini) after one vertical adjustment.
I uninstalled the game, deleted IL-2 Sturmovik Battle of Stalingrad directory, and downloaded it fresh with fresh 12.5 mod (also tried with jsgme) - still same problem.
What else can i try?