There was a report about the same behavior you described and as per OP it was fixed in SU5: Ocean Waves visible in menu, but disappear when the flight loads. Seems to be the same issue than reported here even if the menu screen is not mentioned.
There was a report about the same behavior you described and as per OP it was fixed in SU5: Ocean Waves visible in menu, but disappear when the flight loads. Seems to be the same issue than reported here even if the menu screen is not mentioned.