For me, turning on "UT Exclusions for default scenery" causes the "trees in the bay" phenomenon. While at Juneau, I tried several variations, with FTX Central on default, and also set on North America. I also tried deactivating the Tongass Fjords, (and also repair of TFX) but the result was the same. Trees instead of water with it on, normal water with it off. See if it's the same for you. I am referring to the "Ultimate Terrain X: Alaska" program in particular. Oh, I also moved the entry to various locations in my scenery library list, with no change.
So, while all the other components of UTX AK will display, although not properly, the UT Exclusions for default scenery causes the ocean to dry up completely. The buildings near the shoreline don't match the terrain, and there are also cruise ships up on land. Maybe it's just me?