Heya Batman,
Have you recently installed the new cloud textures by Mike Woolsey found here:
http://www.simviation.com/fs2004scenery29.htmI had the EXACT same problem after installing these cloud textures. I tried about four things and found a fix. So tell me do you have the waterzone extended water effects add-on installed also?
In my case I discovered that (for some unknown reason)there was a conflict in textures if one installs the new cloud textures OVER the Waterzone effects.
What I did was restore the default MS 2004 cloud and water textures from backups. I then re-installed the add-ons in this order:
1. New Cloud Textures
2. Waterzone Effects
FS 2004 has worked like a champion for me since.