Command Formatting Algorithm Issues?

I was working on an algorithm for an admin commands system, that basically formatted a message into something that can be read by the command runner.

local Prefix = ';'
local BatchKey = '|'
local SplitKey = ' '

function RunMessage(Player, Message)
	Message = string.lower(Message)
	local Batches =  {}
	local BatchStarts = {}
	if string.sub(Message, 1, 3) == '/e ' then
		Message = string.sub(Message, 4)
	end
	if not string.sub(Message, 1, string.len(Prefix)) == Prefix then
		return
	else
		table.insert(BatchStarts, 1)
	end
	for Index = string.len(Prefix)+1, string.len(Message) do
		if string.sub(Message, Index, Index+string.len(BatchKey)) == BatchKey then
			if string.sub(Message, Index+string.len(BatchKey)+1, Index+string.len(BatchKey)+1+string.len(Prefix)) == Prefix then
				table.insert(BatchStarts, Index+string.len(BatchKey)+1)
			end
		end
	end
	for Index, BatchStart in pairs(BatchStarts) do
		local BatchEnd
		if string.sub(Message, BatchStart, BatchStart+string.len(Prefix)) then
			BatchEnd = BatchStarts[Index+1]
		else
			BatchEnd = string.len(Message)
		end
		table.insert(Batches, string.sub(Message, BatchStart, BatchEnd))
	end
	for Index, Command in pairs(Batches) do
		local Arguments = {}
		for Argument in string.gmatch(Message, '([^'..SplitKey..']+)') do
			table.insert(Arguments, Argument)
		end
		local CommandName = string.sub(Arguments[1], string.len(Prefix)+1)
		table.remove(Arguments, 1)
		API:RunCommand(Player, CommandName, Arguments)
	end
end