Why are parts disappearing when rounding positions?

For the last while now, I have been working on a building system for my game. I used a tutorial to make the basis for it. As the blocks I am placing with are 4x4, I want to snap the placing position of the block to 4 studs. I have tried to do this but every time it has glitched strangely. The map you place on is randomly generated.

What is happening is that tiles that have been generated randomly disappear where my mouse cursor is.

How can I fix this?

Here is my generation code in a server script:

local partspawn = 1950
local partcount = math.round((partspawn / 10) * 12)
local mapgenerateplace = Vector3.new((partspawn / 2) - partspawn, 0, (partspawn / 2) - partspawn)

local wk,pl = game:GetService("Workspace"),game:GetService("Players")

function spawnmap()
    local db = false
    local folder = Instance.new("Folder")

    folder.Name = "Map"
    folder.Parent = wk

    for i = 1,partcount,1 do
        local newpart = Instance.new("Part",folder)
        local height = math.round((math.random(10, 40) / 8)) * 8
        local rad = math.round(math.random(1, 8))

        if rad == 1 then
            newpart.Color = Color3.fromRGB(100, 100, 106)
            newpart.Material = Enum.Material.Slate
            newpart.Name = "Stone"
            newpart.Size = Vector3.new(40, height, 40)
        else
            newpart.Color = Color3.fromRGB(40, 127, math.round(math.random(70, 110)))
            newpart.Material = Enum.Material.Grass
            newpart.Name = "Grass"
            newpart.Size = Vector3.new(40, height, 40)
        end

        newpart.Position,newpart.Anchored = Vector3.new(mapgenerateplace.X + math.round(math.random(1, partspawn) / 40) * 40, math.round(mapgenerateplace.Y), mapgenerateplace.Z + math.round(math.random(1, partspawn)  / 40) * 40),true

        if newpart then
            local clone = game.ReplicatedStorage.MapObjects.Tree:Clone()
            clone.Parent = workspace

            if newpart.Touched then
                if db == false then
                    local parts = newpart:GetTouchingParts()

                    for i, v in pairs(parts) do
                        if v.Position == newpart.Position then
                            newpart:Destroy()
                            clone:Destroy()
                        end
                    end
                end
            end

            if math.random(0, 4) == 1 then
                if clone:FindFirstChild("Trunk") then
                    clone.Trunk.Position = Vector3.new(newpart.Position.X, newpart.Position.Y + height / 2, newpart.Position.Z)

                    clone.Leaves.Position = Vector3.new(clone.Trunk.Position.X, clone.Trunk.Position.Y + 10.5, clone.Trunk.Position.Z)
                else
                    clone:Destroy()
                end
            else
                clone:Destroy()
            end
        end
    end

    db = false
end
spawnmap()

Here is my placement code in a local script:

local replicatedStorage = game:GetService("ReplicatedStorage")
local UIS = game:GetService("UserInputService")
local runService = game:GetService("RunService")

local placeStructure = replicatedStorage:WaitForChild("PlaceStructure")
local structureFrame = script.Parent.BuildFrame
local structures = replicatedStorage:WaitForChild("Structures")

local player = game.Players.LocalPlayer
local char = player.Character or player.Character:Wait()
local humanoidRootPart = char:WaitForChild("HumanoidRootPart")
local mouse = player:GetMouse()

local yBuildingOffset = 0
local maxPlacingDistance = 50

local rKeyIsPressed = false
local placingStructure = false

for _, structureButton in pairs(structureFrame:GetChildren()) do
    if structureButton:IsA("TextButton") then
        structureButton.MouseButton1Up:Connect(function()

            structureFrame.Visible = false
            structureFrame.Parent.Delete.Visible = false
            script.Parent.Instructions1.Visible = true
            script.Parent.Instructions2.Visible = true

            local yOrientation = 0

            local goodToPlace = false
            local placedStructure

            if placingStructure == false then
                placingStructure = true

                local clientStructure = structures:FindFirstChild(structureButton.Name):Clone()
                clientStructure.BrickColor = BrickColor.new("Forest green")
                clientStructure.Material = "Neon"
                clientStructure.CanCollide = false
                clientStructure.Parent = workspace

                yBuildingOffset = clientStructure.Size.Y / 2

                local startingCFrame = CFrame.new(0, 0, 0)
                clientStructure.CFrame = humanoidRootPart.CFrame:ToWorldSpace(startingCFrame)

                runService.RenderStepped:Connect(function()
                    local mouseRay = mouse.UnitRay
                    local castRay = Ray.new(mouseRay.Origin, mouseRay.Direction * 1000)
                    local ignoreList = {clientStructure, char}
                    local hit, position = workspace:FindPartOnRayWithIgnoreList(castRay, ignoreList)

                    if hit and (not hit:IsA("Terrain") or not hit.Name:lower() == "terrain") and (humanoidRootPart.Position - clientStructure.Position).Magnitude < maxPlacingDistance then
                        goodToPlace = true
                        clientStructure.BrickColor = BrickColor.new("Forest green")
                    else
                        goodToPlace = false
                        clientStructure.BrickColor = BrickColor.new("Crimson")
                    end

                    local newAnglesCFrame = CFrame.Angles(0, math.rad(yOrientation), 0)
                    local newCFrame = CFrame.new(position.X, position.Y + yBuildingOffset, position.Z)
                    local cframeTable = table.pack(newCFrame:GetComponents())

                    --Set the Position

                    for i, v in pairs(cframeTable) do
                        --Edit:

                        cframeTable[i] = math.round(v / 4) * 4
                    end

                    local roundedCFrame = CFrame.new(table.unpack(cframeTable))
                    clientStructure.CFrame = roundedCFrame * newAnglesCFrame

                    --Positon Set
                end)

                UIS.InputBegan:Connect(function(input)
                    if input.KeyCode == Enum.KeyCode.R then
                        rKeyIsPressed = true

                        local rotationSpeed = 5
                        while rKeyIsPressed do
                            wait()
                            if placingStructure == true then
                                yOrientation = yOrientation + math.deg(0.785398)

                                wait(0.25)
                            end
                        end
                    end
                end)

                UIS.InputEnded:Connect(function(input)
                    if input.KeyCode == Enum.KeyCode.R then
                        rKeyIsPressed = false
                    end
                end)

                local inputConnection

                inputConnection = UIS.InputBegan:Connect(function(input)
                    if input.UserInputType == Enum.UserInputType.MouseButton1 and placingStructure == true then
                        if goodToPlace then
                            local structureCFrame = clientStructure.CFrame
                            placedStructure = placeStructure:InvokeServer(clientStructure.Name, structureCFrame)

                            if placedStructure then
                                placingStructure = false
                                clientStructure:Destroy()
                                structureFrame.Visible = true
                                script.Parent.Instructions1.Visible = false
                                script.Parent.Instructions2.Visible = false
                                inputConnection:Disconnect()
                            end
                        end
                    end
                end)

                UIS.InputBegan:Connect(function(input)
                    if input.KeyCode == Enum.KeyCode.X then
                        placingStructure = false
                        clientStructure:Destroy()
                        structureFrame.Visible = true
                        script.Parent.Instructions1.Visible = false
                        script.Parent.Instructions2.Visible = false
                        inputConnection:Disconnect()
                    end
                end)                
            end         
        end)
    end
end