Im a new x5 owner and having a few problems

I recently went to BMW to have a few options turned on the computer (autolock doors etc)
After waiting an hour the master engineer, i think he was, told me that they couldnt communicate with the car and was probably because i had taken out the stereo and MID controller (under the business cd). Is this correct and if so how have others who have fitted there own stereos solved this?
Another issue, possibly related, is that the stalk controls work intermitantly. I have the correct loom and stalk adaptor and has been fitted professionally but we are all at a loss!!
Hoping somebody can help me with these issues..
thanks