I was looking into why some of the rivers were acting strangely and I noticed there are a few errors in the stamp data...I'll update this post from time to time

fixed the scrapyard data...https://dl.dropboxusercontent.com/u/75549875/Fallen%20Enchantress/StampFixes/S_Scrapyard_Blank_01.zip

The scrapyard had this issue

if you see the waterfall in the water... Simple fix

Tile Number (31,9) is a submerged tile... Removed from <MapRiverData> section
Tile Number (30,9) was labeled as river sub-terrain land, changed to <TerrainType>Cliff<\TerrainType>

Thus, we get this result instead

There are many issues in the file S_Northern_Wastes_Blank_01.xml

There are a lot of supposed river tiles that are not actually defined as river tiles... and rivers that end not on a cliff edge causing land endings.