So I brought my car in today and just got a call from my dealer (who I bought the car from) saying:
- they did not find any chip so not sure what other dealer was about
- will fix my gearbox (update the software - fingers crossed it will fix the issue once and for all)
- will do that under the warranty
So the moral of this story from my point of view is following:
- the dealer you bought your car from should be the first point of contact. On one hand their are somehow liable for what they sold to you and on the other already done business with you therefore generally more friendly and happy to help.
- despite the single BMW warranty it appears that if a dealer doesn't want to do the warranty repairs they will find a reason (the other dealer before referring to a "chip" and sending me to the dealer I bought the car from tried to tell me that the problem could be due to the 19" 313 wheels - which are factory spec therefore just plain silly)
- if you are told that the car is / was modified it not necessarily the case. As Eelesy24 pointed above it could be just a glitch as well as the dealer being just not too keen on doing the warranty work
You got to love amazing BMW after sales service and warranty - to be fair will think twice now before buying another BMW.
Thank you all for your help and advice!