I think you hit the nail on the head there my friend, last time i looked at coding keys i had been working on van all day and had a flat battery a few hours earlier, i only jumped it and let it run for a while but hadnt actually charged it !
Revisited this today and adaptions were working as expected, channel 00 cleared stored keys (not sure this is actually necessary) then giving channel 01 a 0 value and saving allows you to add one key, repeat channel 01 until all keys are added
Now for the next problem, the new and old fobs all work for locking and unlocking the van but the new fob doesnt do anything to the elec side door

I had assumed, incorrectly, that when the fob was adapted it would also work the side door, i have found
this vcds document that talks about an adaption channel in the side door control module that has a bearing the key/fob but not sure if this is relevant as a) its from a T5 2004-2009 and b) it implies the fob has two buttons, one for open and one for close ?
So now i am trying to figure out if the issue is with the side door module or if my BCM is not coded/adapted correctly, i did originally have to make two coding changes to allow the locking status and the door position status to be sent (or allowed) over the canbus so it seems possible theres another change required to allow the open/close signal over canbus also ?
If anyone has any thoughts on this it would be appreciated, failing that i may start a thread on ross tech forum and see if they have any input, theres lots of info around about key adaptions but nothing in conjunction with electric doors ?