Try this.... disconnect battery for a while (10 mins or so) then when you reconnect hold the keyfob button down for like 5-7 seconds... this programs the alarm to the keyfob control and it should put everything back in sync... this advice was given to me by a VW main stealer..... and works for me.
Could be that your sparkers are not firing on all six.... check each one for a healthy spark.. you will know a healthy spark if when holding the disconnected lead with the engine running you receive a mighty sharp jolt down your spine
As a further safety note... I really do NOT recommend doing the above as you could do yourself harm.. and will almost certainly damage your cars 'brain' ... sorry !!!