STEP 1: Insert Microsoft FS2004 CD1 into your cd drive.
STEP 2: Go into 'My Computer', right click FS_DISK1 and then select explore.
In the new window which displays the contents of the disc, double click
on 'MSGAME1.cab'. (It might have a symbol of a blue filing cabinet)
(Make sure your items are being displayed in alphabetical order) Scroll
down to the letter F and look for the words beginning in FX. Scroll
through the words beginning with fx until you find the 2 files called
'fx_contrail_l.fx' and 'fx_contrail_s.fx'.
STEP 5: Finally copy the 2 files to C:Program files/microsoft games/flight simulator 9/effects folder and overwrite when prompted.
Now your contrails will be normal again
Thanks to CAT19_Hitman for the two contrail pictures