I purchased a used 2006 Mini Cooper S Conv with 76000 miles on it from a Mini dealership in Virginia 9 months ago. No extended warranty was offered at time of purchase. I am currently experiencing an automatic transmission problem with the Aisin 6-speed with 84,000 miles on the odometer. My wife had two near miss accidents and I had one near miss, because the automatic transmission wants to go onto neutral shifting 2nd to 3rd gear the engine will go to 4000-5000 RPM and you don’t know when it will happen. When it does happen you get no EML or EPS lights. It will eventually go into gear with a bang. My has wife experienced this while pulling out into the fast lane of highway traffic. I have filed a report with NHTSA, because of the safety nature. So, the Mini dealership has had the car for the last week on last Friday late in the afternoon the AS called to tell me I need a new transmission and the dealership wanted $9600.00 to fix, I told them that it was too much (since I paid $16000.00 for the car) and would have to lower the repair cost. My last negotiation with the dealership today they came down from $8300, then to $8000, to now $7600.00. This is still too much to pay since I paid $16000.00. I found a local Mini repair shop that gave me an estimate of $5000 to do the transmission repair, which is a factory remanufactured automatic transmission with a warrranty. This shop also told me he had to go with a reman automatic transmission because he can’t get internal parts from the dealership because Mini does not list internal parts in the parts their manuals, Mini wants you to purchase a whole new transmission

 

unfortunately theres more then you having the issues with the tranny

yes mini only sells entire trannys so you are at their mercy (or another company that remans them )
02-08 MINI COOPER REMANUFACTURED/REMAN AUTOMATIC CVT TRANSMISSION | eBay

 

I'm not sure this is going to help Mary at this point since it has been over a year now since the original post but being that she is from Virginia too like me I'd thought I try and help.

I had similar problems as Marys-06Mini in my '06 Mini Cooper S convertible. My issues came up after driving the car for a while and getting up to running temperature. The transmission would slip between 2nd, 3rd and 4th gear. I tried 5 fluid changes which seemed to help very little. I finally came upon a post where someone changed out their valve body which fixed the problem. I did the same and wrote up a DIY pictorial which I hope helps others in this situation. I'm not sure if I can post a link to another site here but if you google search

Aisin 6 Speed AUTOMATIC, failed at 80K?

MCSA - Aisin 6 Speed AUTOMATIC, failed at 80K? - Page 9 - North American Motoring

you'll find my write up starting at post #223. Good luck to others that have tried the transmission fluid change that didn't help and need to try a valve body swap.