Hi jr birdman.
As Gary says, there are two .fx files that control the contrail effects. However, as the effect is showing (as cubes) then these files are likely to be still there.
In the 'effects' folder is a subfolder called 'texture' - in this folder there are two .bmp files (fx_1.bmp and fx_smoke.bmp) used by the contrail .fx files to render the visuals correctly. If you're seeing cubes then you should check that the .bmp files are still there. If not, you can retrieve them from your original discs.
If you download my AutoEnvironment pack from the downloads section, it includes replacement 3D contrails that look much better then the 2D defaults.
