Ok, I had a 2006 S, but HATED the run flats and no spare, traded it for a base 07 with a 6 speed. Once in about 8 - 10 shifts from (ONLY) 1st to 2nd gear, occasionally it grinds into 2nd. CLUTCH FULLY DEPRESSED, sometimes only at 12 mph?? Never on downshift from 3rd to 2nd, only on 1st to 2nd upshift. I do not use my tranny to slow me down, I read somewhere that brakes are cheaper than trannies. My Mini Does Not have to be in "sport" mode, happens in or out or sport selected. -- I took it to Mini in Bloomington MN, they said, after 4 hours of test driving, that...quote..."We could create the grinding sound you heard, but only if we shifted too quickly between first and second gear". unquote. I asked "how quickly is too quickly?" and why doesn't it happen betw 3 and 4 or more easily betw 5 & 6 which are a straight shot? They said they did not know. said it was "MY ERROR??"
I NEVER had this in my 06 "S". I know, different tranny, different response in an "S". But why only 1st to 2nd gear? I like my base Mini with regular tires and ummmmm A SPARE! I am getting 42 miles to the gallon...proven at the pump, running premium-91 to 93 octane, (USA) (podunk usa at that) at approx 75-85 mph highway depending on copper poppers (police on side of road), for approx 3 1/2 hrs one way between La Crosse WI and Milwaukee WI, 15" conti worn out stock rubbers, (SOON TO BE 16" MINI WHEELS) sunroof open, radio on max volume playing "THE HEAVY - HOW YOU LIKE ME NOW??" I strongly suggest before jumping into your morning commute, you pu t that song on...or Timo Maas "To Get Down" or Paul Oakenfold "Ready-Steady-GO!" -- in 2 versions, English and KOREAN which, if you watch movies with Minis in them, these songs are PARAMOUNT!!!

 

Yeah gear shifts can be a problem, I had a Honda Civic SI that sort of did the same thing as yours, though mainly when things were very warm. I used to "ease" the shift lever between the 2 gears with a double clutch and a brief pause in neutral. Turned out to have a weak synchro. Never had any reason to downshift 2nd to 1st very often so don't remember that being a problem.

 

It will continue to get worse, expecially during cold weather, say 40F and below. It took me almost a full year to prove to my dealship that I had an issue and just recently in January they finally agreed there was an issue and warrantied my transmission; 300 miles to warranty. Good luck and keep at them! Also, there is a thread from a year or so back about this subject with multiple people replying with the same issue. I'll look and post back if I can find it.

 

Found the other thread.

https://www.northamericanmotoring.co...t-grind-4.html