Why isnt this DataStoring script saving my 2nd value?

The problem is the way you are saving the data, one key can only hold one value. Setting the key again overwrites the previous value stored.

game.Players.PlayerRemoving:connect(function(plr)
    local uniquekey = "id-"..plr.userId
    local SaveCoins = {plr.leaderstats.Coins.Value}
    local SaveRegular = {plr.Regular.Value}
    -- data saved 
    DSService:SetAsync(uniquekey,SaveCoins)
    -- data overwritten 
    DSService:SetAsync(uniquekey,SaveRegular)
end)

Other notes:-

You should be checking the data that is being loaded as there is still a possibility of it being nil, we can simply use plrData[1] or 0 which will return 0 if the first argument is nil.

It is best to create a function for saving and loading as this is usually done on multiple occasions so we can just reuse the function.

There are a lot of possible errors which can also occur which are not managed in the example below.

Example:-

local dsServ = game:GetService('DataStoreService')
local dataStore = dsServ:GetDataStore(' name of data store')

local function getKey(plr)
    return "id-"..plr.userId
end

local function loadData(plr)
    return dataStore:GetAsync(getKey(plr))
end

local function saveData(plr, data)
    dataStore:SetAsync(getKey(plr), data)
end

game.Players.PlayerAdded:connect(function(plr)
    local leaderstats = Instance.new("IntValue")
    leaderstats.Name = "leaderstats"

    local savevalue = Instance.new("IntValue", leaderstats)
    savevalue.Name = "Coins"

    local Regular = Instance.new("IntValue")
    Regular.Name = "Regular"

    -- it is more efficent to set the parents last
    -- http://devforum.roblox.com/t/psa-dont-use-instance-new-with-parent-argument/30296
    leaderstats.Parent = plr
    Regular.Parent = plr

    local plrData = loadData(plr)
    if plrData then
        savevalue.Value = plrData[1] or 0
        Regular.Value = plrData[2] or 0
    else
        savevalue.Value = 1000000
        Regular.Value = 0
        saveData(plr, {savevalue.Value, Regular.Value})
    end
end)

game.Players.PlayerRemoving:connect(function(plr)
    saveData(plr, {plr.leaderstats.Coins.Value, plr.Regular.Value})
end)

I hope this helps.