Random map loading is not random?

Don't call math.randomseed(tick()) in your function. Just call it at the top of your script or else it will choose the same number over and over.

math.randomseed(tick())  --moved it to the start of your script

function loadMap(x)
    local maps = Maps:GetChildren()
    for i = 1, #maps do
        if maps[i].Value == x then
            print(maps[i].MapName.Value)
            maps[i].Model.Parent = game.Workspace
        end
    end
end

function loadRandomMap()
    local mapNum = math.random(Options.Maps.Value)
    if mapNum == System.CurrentMap.Value then
        local mapNum = math.random(Options.Maps.Value)
    end 
    System.CurrentMap.Value = mapNum
    loadMap(mapNum)
end

local Updates = 10000
local seeder = coroutine.create( function() for int = 1, Updates do math.randomseed(tick()) coroutine.yield() end end)


coroutine.resume(seeder)--Use this line of code everytime you want to get a random number

Try this instead:

local Updates = 10000
local seeder = coroutine.create( function() for int = 1, Updates do math.randomseed(tick()) coroutine.yield() end end)

function loadMap(x)
    local maps = Maps:GetChildren()
    for i = 1, #maps do
        if maps[i].Value == x then
            print(maps[i].MapName.Value)
            maps[i].Model.Parent = game.Workspace
        end
    end
end

function loadRandomMap()
coroutine.resume(seeder)
    local mapNum = math.random(Options.Maps.Value)
    if mapNum == System.CurrentMap.Value then
coroutine.resume(seeder)
        local mapNum = math.random(Options.Maps.Value)
    end 
    System.CurrentMap.Value = mapNum
    loadMap(mapNum)
end