I have had a small issue of adding an extra key also ( remote part ) but I finally managed to do it with no problems. Anyway, the info on ross-tech website is a bit wrong, at least for the 409.1 version I have used.
Here's how I did it. I have a 2002 A4 B6 so my key adding is found under 46.Central Conv. / Adaptation / Chan 21 ( a friend's VW had it in 35-Centr.Locking/Adaptation/Chann 1 - so test to see where it is on your model ).
The number was 0 on the channel and according to ross-tech website that was the number of keys already matched. It was a wrong info as I already had my old key working fine so it wasn't possible for that 0 to mean that. After I deleted all the entries by saving 0 in the channel 00, I went to chan 21 and pressed the UP button once so the number became 1 instead of 0. It's normal for the TEST button to gray out because if you use the arrow keys it automatically TESTs the value ( only if you input it via keyboard you will have to press TEST as the software doesn't know if you want to TEST chan 1 or you input for example a 5 after that to test chan 15 - so it's NORMAL ). So ... having the 1 value automatically tested and working by only pressing the UP button once, the upper fields could read KEY and ADJUSTING - or something, I am giving this info from my memory, I don't have the VAGCOM in front right now. Ross-tech is telling us to PRESS SAVE and then the button on the remote but that is WRONG. So don't press SAVE at this point, just press and hold for 1 second the UNLOCK button on your remote and it will change from ADJUSTING to LEARNED ( or REGISTERED - I don't recall exactly ). Now you DO NOT PRESS SAVE as ross-tech WRONGLY says. You press the UP button again so the number will become from 1 to 2. The upper field will read ADJUSTING again and you press the UNLOCK on the 2nd remote and it will change from ADJUSTING TO LEARNED ( or REGISTERED of course ). If you have 3 keys you will repeat this step. Once you have ALL KEYS registered you NOW PRESS SAVE. So the SAVE button is pressed ONLY when all keys have been registered. Test all keys after that. It will work 100%.
Ross-Tech info found here:
http://www.ross-tech.com/vag-com/cars/vw-remote-matching.html was wrong for my 409.1 VAG-COM version. It may work for other versions or other car models but as I said, mine worked like this.
Good luck.