ALERT: I have downloaded the wakes a it appears that all of the particle statements are missing the Ground Decal statement: Ground Decal=1 therefore when in P3D and the sea is high, the wake will be below the water or appear to be broke in pieces.
An Example:
[Particle.1]
Lifetime=34.0, 34.0
Type=21
X Scale=7.0, 7.0
Y Scale=10.0, 10.0
Z Scale=0.00, 0.00
X Scale Rate=0.06, 0.06
Y Scale Rate=0.08, 0.08
Drag=0.00, 0.00
Color Rate=0.00, 0.00
Fade In=0.05, 0.05
Fade Out=0.70, 0.70
Ground Normal=1
Ground Decal=1
Shade=1
Face=1, 0, 1
NOTE: The attached zip should have the correct statements.