diff --git a/GPU/D3D11/DrawEngineD3D11.cpp b/GPU/D3D11/DrawEngineD3D11.cpp
index 9ef139486f..73708c930a 100644
--- a/GPU/D3D11/DrawEngineD3D11.cpp
+++ b/GPU/D3D11/DrawEngineD3D11.cpp
@@ -581,7 +581,11 @@ rotateVBO:
 		}
 	} else {
 		PROFILE_THIS_SCOPE("soft");
-		decOptions_.applySkinInDecode = true;
+		if (!decOptions_.applySkinInDecode) {
+			decOptions_.applySkinInDecode = true;
+			lastVType_ |= (1 << 26);
+			dec_ = GetVertexDecoder(lastVType_);
+		}
 		DecodeVerts(decoded);
 		bool hasColor = (lastVType_ & GE_VTYPE_COL_MASK) != GE_VTYPE_COL_NONE;
 		if (gstate.isModeThrough()) {
@@ -653,7 +657,7 @@ rotateVBO:
 		if (result.action == SW_DRAW_PRIMITIVES) {
 			D3D11VertexShader *vshader;
 			D3D11FragmentShader *fshader;
-			shaderManager_->GetShaders(prim, lastVType_, &vshader, &fshader, pipelineState_, false, false, decOptions_.expandAllWeightsToFloat, decOptions_.applySkinInDecode);
+			shaderManager_->GetShaders(prim, lastVType_, &vshader, &fshader, pipelineState_, false, false, decOptions_.expandAllWeightsToFloat, true);
 			context_->PSSetShader(fshader->GetShader(), nullptr, 0);
 			context_->VSSetShader(vshader->GetShader(), nullptr, 0);
 			shaderManager_->UpdateUniforms(framebufferManager_->UseBufferedRendering());
diff --git a/GPU/Directx9/DrawEngineDX9.cpp b/GPU/Directx9/DrawEngineDX9.cpp
index 1e6bd62d61..f16d48c6a8 100644
--- a/GPU/Directx9/DrawEngineDX9.cpp
+++ b/GPU/Directx9/DrawEngineDX9.cpp
@@ -546,7 +546,11 @@ rotateVBO:
 			}
 		}
 	} else {
-		decOptions_.applySkinInDecode = true;
+		if (!decOptions_.applySkinInDecode) {
+			decOptions_.applySkinInDecode = true;
+			lastVType_ |= (1 << 26);
+			dec_ = GetVertexDecoder(lastVType_);
+		}
 		DecodeVerts(decoded);
 		bool hasColor = (lastVType_ & GE_VTYPE_COL_MASK) != GE_VTYPE_COL_NONE;
 		if (gstate.isModeThrough()) {
@@ -618,7 +622,7 @@ rotateVBO:
 
 		ApplyDrawStateLate();
 
-		VSShader *vshader = shaderManager_->ApplyShader(false, false, lastVType_, decOptions_.expandAllWeightsToFloat, decOptions_.applySkinInDecode, pipelineState_);
+		VSShader *vshader = shaderManager_->ApplyShader(false, false, lastVType_, decOptions_.expandAllWeightsToFloat, true, pipelineState_);
 
 		if (result.action == SW_DRAW_PRIMITIVES) {
 			if (result.setStencil) {
diff --git a/GPU/GLES/DrawEngineGLES.cpp b/GPU/GLES/DrawEngineGLES.cpp
index 2c0c54304d..14eb57afc7 100644
--- a/GPU/GLES/DrawEngineGLES.cpp
+++ b/GPU/GLES/DrawEngineGLES.cpp
@@ -267,7 +267,7 @@ void DrawEngineGLES::DoFlush() {
 	GEPrimitiveType prim = prevPrim_;
 
 	VShaderID vsid;
-	Shader *vshader = shaderManager_->ApplyVertexShader(CanUseHardwareTransform(prim), useHWTessellation_, lastVType_, decOptions_.expandAllWeightsToFloat, decOptions_.applySkinInDecode, &vsid);
+	Shader *vshader = shaderManager_->ApplyVertexShader(CanUseHardwareTransform(prim), useHWTessellation_, lastVType_, decOptions_.expandAllWeightsToFloat, decOptions_.applySkinInDecode || !CanUseHardwareTransform(prim), &vsid);
 
 	GLRBuffer *vertexBuffer = nullptr;
 	GLRBuffer *indexBuffer = nullptr;
@@ -331,7 +331,11 @@ void DrawEngineGLES::DoFlush() {
 		}
 	} else {
 		PROFILE_THIS_SCOPE("soft");
-		decOptions_.applySkinInDecode = true;
+		if (!decOptions_.applySkinInDecode) {
+			decOptions_.applySkinInDecode = true;
+			lastVType_ |= (1 << 26);
+			dec_ = GetVertexDecoder(lastVType_);
+		}
 		DecodeVerts(decoded);
 
 		bool hasColor = (lastVType_ & GE_VTYPE_COL_MASK) != GE_VTYPE_COL_NONE;
diff --git a/GPU/GLES/ShaderManagerGLES.cpp b/GPU/GLES/ShaderManagerGLES.cpp
index aa17822d8c..1f75b7412b 100644
--- a/GPU/GLES/ShaderManagerGLES.cpp
+++ b/GPU/GLES/ShaderManagerGLES.cpp
@@ -789,7 +789,7 @@ Shader *ShaderManagerGLES::ApplyVertexShader(bool useHWTransform, bool useHWTess
 
 			// Can still work with software transform.
 			VShaderID vsidTemp;
-			ComputeVertexShaderID(&vsidTemp, vertType, false, false, weightsAsFloat, useSkinInDecode);
+			ComputeVertexShaderID(&vsidTemp, vertType, false, false, weightsAsFloat, true);
 			vs = CompileVertexShader(vsidTemp);
 		}
 
diff --git a/GPU/Vulkan/DrawEngineVulkan.cpp b/GPU/Vulkan/DrawEngineVulkan.cpp
index c1d1871140..bc51195144 100644
--- a/GPU/Vulkan/DrawEngineVulkan.cpp
+++ b/GPU/Vulkan/DrawEngineVulkan.cpp
@@ -841,7 +841,11 @@ void DrawEngineVulkan::DoFlush() {
 		}
 	} else {
 		PROFILE_THIS_SCOPE("soft");
-		decOptions_.applySkinInDecode = true;
+		if (!decOptions_.applySkinInDecode) {
+			decOptions_.applySkinInDecode = true;
+			lastVType_ |= (1 << 26);
+			dec_ = GetVertexDecoder(lastVType_);
+		}
 		DecodeVerts(decoded);
 		bool hasColor = (lastVType_ & GE_VTYPE_COL_MASK) != GE_VTYPE_COL_NONE;
 		if (gstate.isModeThrough()) {
@@ -924,7 +928,7 @@ void DrawEngineVulkan::DoFlush() {
 				VulkanFragmentShader *fshader = nullptr;
 				VulkanGeometryShader *gshader = nullptr;
 
-				shaderManager_->GetShaders(prim, lastVType_, &vshader, &fshader, &gshader, pipelineState_, false, false, decOptions_.expandAllWeightsToFloat, decOptions_.applySkinInDecode);
+				shaderManager_->GetShaders(prim, lastVType_, &vshader, &fshader, &gshader, pipelineState_, false, false, decOptions_.expandAllWeightsToFloat, true);
 				_dbg_assert_msg_(!vshader->UseHWTransform(), "Bad vshader");
 				VulkanPipeline *pipeline = pipelineManager_->GetOrCreatePipeline(renderManager, pipelineLayout_, pipelineKey_, &dec_->decFmt, vshader, fshader, gshader, false, 0);
 				if (!pipeline || !pipeline->pipeline) {