FSX does that with me where it puts the contrails sideways!
Yes, it's because in FSX, the coordinates are not in the same order.
In FS9, it was height, longitude and latteral (or something like that).
In FSX, it's now longitude, latteral and finally height.
This is why the smoke systems from the FS9 planes are usually in the wrong place when you import the plane into FSX. You simply need to edit the aircraft.cfg to change the order of the coordinates.
Also, this contrail effect is useless in FSX, because FSX automatically creates contrails at the end of the wings, for any plane automatically, so you can safely remove the contrails effects from the aircraft.cfg.