Missing Water Tiles

Hi, so I asked this question on the original Forum for Pokemon Essentials on the wiki when it still existed but now that it doesn't I will have to ask it here. There are these water tiles that I put down on the map of my starter town and it makes a really nice little river that goes through the starter town. But when I run the game it doesn't show up. The bridges that I put are still there but nothing else is. The river is on the second layer and the bridges are on the third and everything on the second layer looks fine. i tried compiling the data (which ended in a whole fiasco when it cam to the tm.txt since I changed some names, but it was fixed in the end) but they still didn't show up. Here are some screenshots in the mode where you work on things and the game itself. I can't post images at this point but when I get past 5 posts I will.

Here are the pictures!

Does anyone know what is happening? Please!

This was happening to me too, I'm not sure what's causing it, but I was able to make my water appear in game by having it be the only tile on each layer instead of having grass on the first layer and then water on other layers, once I did that the water showed up in game.