I've run out of things to check and going a bit crazy at this time. Here's my dilemma.
2008 Mini Cooper R55 Clubman S

I purchased the Key Fob from Amazon, Xtools Pad 3 kit (with KC-100). When I bought the car, the only fob they had was the Comfort Access Fob.

I was able to update the CAS and get the new key listed in position #3. Tool says all is good, but I am not able to unlock doors, or start car with fob in ignition slot.
First though.. Maybe I have a bad key? I did by it on Amazon for $40. So, I also have a 2013 that has two working (non-comfort access) keys. I was able to successfully get this $40 key programmed to the 2013. Starts car and unlocks/locks doors.
One thought was, a bad ignition switch slot (not getting code from fob?). Swapped them and no change and I know the one works 100%. I linked the new key with the known working ignition slot, same results.
The CAS is suspect, but I don't know how to determine that as it did take the new key, the update, and does with with the Comfort Access key. While it could be this, I'm not certain based on typical CAS issues I have read about.

So, in short, verified ignition slot is ok, CAS appears fine, but still questionable. Car starts with Comfort access key I had when purchasing car.

At this point, I will take any and all suggestions and anyone familiar with the XTools Pad 3, I can even take suggestions of what I can try on that. Also, all codes brought on by updating CAS were cleared prior to programming.
Thanks in advance for any help/suggestions.
Tim