If it's like my old Golf (which it might be, being VAG), you need to make sure you engage the key in the ignition pretty quickly after manually unlocking and opening the car, otherwise it won't work.
Also, I'm sure I read that the keys (even the non-flip spares) have some kind of transponder/electronics in them... so copies cut from the spare using a traditional key cutter service won't disable the alarm properly even if the physical key bit is absolutely identical to the original. Not sure how accurate that info is as I can't remember where/when I read it, sorry!