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Pick function no longer works after applying multiple viewports

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Here is my pick function which worked fine with one viewport, but doesn't now that I use two viewports. I passed the width of each viewport instead of the entire screen too, but that didn't work.
// Get the ray from mouse pos
	D3DXMATRIXA16 matProj;
    device->GetTransform(D3DTS_PROJECTION, &matProj);

    POINT ptCursor;
	ScreenToClient(hWnd, &ptCursor);

	// Compute the vector of the pick ray in screen space
	v.x =  (((2.0f * ptCursor.x) / width) - 1) / matProj._11;
	v.y = -(((2.0f * ptCursor.y) / height) - 1) / matProj._22;
	v.z =  1.0f;

	// Get the inverse of the composite view and world matrix
	D3DXMATRIXA16 matView, matWorld, m;
	device->GetTransform(D3DTS_VIEW, &matView);
	device->GetTransform(D3DTS_WORLD, &matWorld);
	m = matWorld * matView;
	D3DXMatrixInverse(&m, NULL, &m);

	// Transform the screen space pick ray into 3D space
	vPickRayDir.x  = v.x*m._11 + v.y*m._21 + v.z*m._31;
	vPickRayDir.y  = v.x*m._12 + v.y*m._22 + v.z*m._32;
	vPickRayDir.z  = v.x*m._13 + v.y*m._23 + v.z*m._33;
	vPickRayOrig.x = m._41;
	vPickRayOrig.y = m._42;
	vPickRayOrig.z = m._43;

	// Get the picked triangle
	bool collision=false;
	// Collect only the closest intersection
	int	index, tempIndex;
	FLOAT fBary1, fBary2, fClosestDist=343.0f;
	D3DXVECTOR3 vTempTri[3];

		for(i=0; i<iNumTriangles; i++){
			vTempTri[0] = pVertices[3*i+0].vPos;
			vTempTri[1] = pVertices[3*i+1].vPos;
			vTempTri[2] = pVertices[3*i+2].vPos;

			if(D3DXIntersectTri(&vTempTri[0], &vTempTri[1], &vTempTri[2], 
								&vPickRayOrig, &vPickRayDir, &fBary1, 
								&fBary2, fDist))
				D3DXVECTOR3 vIntersect = vPickRayOrig+(vPickRayDir*(*fDist));
				bSelected = true;
				if(*fDist < fClosestDist){
					fClosestDist = *fDist;

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Original post by Sfpiano
...I passed the width of each viewport instead of the entire screen too, but that didn't work...

I agree that it is most likely to be screen coords -> ray which is causing the problem.

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