diff --git a/GPU/Directx9/ShaderManager.cpp b/GPU/Directx9/ShaderManager.cpp
index 0084300598..aede525d11 100644
--- a/GPU/Directx9/ShaderManager.cpp
+++ b/GPU/Directx9/ShaderManager.cpp
@@ -633,6 +633,11 @@ LinkedShader *ShaderManager::ApplyShader(int prim) {
 		const LinkedShaderCacheEntry entry(vs, fs, ls);
 		linkedShaderCache_.push_back(entry);
 	} else {
+		// If shader changed we need to update all uniforms
+		if (lastShader_ != ls) {
+			ls->dirtyUniforms = DIRTY_ALL;
+		}
+
 		ls->use();
 	}
 
diff --git a/GPU/Directx9/VertexShaderGenerator.cpp b/GPU/Directx9/VertexShaderGenerator.cpp
index 1f1e7d7e9a..e33b0bad58 100644
--- a/GPU/Directx9/VertexShaderGenerator.cpp
+++ b/GPU/Directx9/VertexShaderGenerator.cpp
@@ -149,17 +149,18 @@ void GenerateVertexShader(int prim, char *buffer, bool useHWTransform) {
 				doLight[i] = LIGHT_FULL;
 		}
 	}
+	
+
+	if (gstate.isModeThrough())	{
+		WRITE(p, "float4x4 u_proj_through;\n");
+	} else {
+		WRITE(p, "float4x4 u_proj;\n");
+		// Add all the uniforms we'll need to transform properly.
+	}
 
 	if (enableFog) {
 		WRITE(p, "float2 u_fogcoef;\n");
 	}
-
-	if (gstate.isModeThrough())	{
-		WRITE(p, "float4x4 u_proj_through:register(c0);\n");
-	} else {
-		WRITE(p, "float4x4 u_proj:register(c8);\n");
-		// Add all the uniforms we'll need to transform properly.
-	}
 	if (useHWTransform || !hasColor)
 		WRITE(p, "float4 u_matambientalpha;\n");  // matambient + matalpha