This car has around 96000 miles but i believe it started having this problem since around 80000 miles.
After driving for long miles 40+ and at highway speeds, it randomly gets rough idles such as when i had to stop for lights.(happens occasionally as some days i don't have it driving the same distance) It runs about 5 seconds by itself and it disappears on command if i press the clutch and add some gas. (i had to do this most of the times so that other drivers won't see the car chugging)

other than this problem, the car runs normal, it accelerates good and never stalled.

Please look at the following link because it sounds like this, starts at around 23 seconds into the video
http://www.youtube.com/watch?v=tUR9xHwtCmI

History of car; has been rearended at 25+ mph and properly serviced by dealer; it is completely stock; used to use citgo 93 gas but switched to shell 93 because i want to long life the car.
Also the car is currently at the dealer for radiator replacement because of leaks, front brake job, belt swap (squealing), oil change, and it is already quoted at $1650 including tax. i am afraid that costs will shoot up high if i include this rough idling problem plus its already friday and too late to call them.

 

Does it happen if the car is idling and in neutral? Is it the original clutch?

 

It doesn't have rough idle when you start up the car in the morning or idle it for a long time after start up such as waiting for the car to warm up. Neutral is the same thing, i remembered after a long drive when i parked the vehicle in a parking lot and put it into neutral, it has the same rough idling for 5 seconds. (this is embarrassing when there are people standing next to me). Clutch is not original, the only reason i included the clutch was because i heard that to rev your engine in idle, you need to press the clutch so you don't damage something.

for instance, this week i haven't noticed any rough idles but last week, monday to be precise, I've experienced it.

 

thats what mini does! it will click when its in neutral with the clutch out but do you know what it is? cause i cant figure it out

 

Does your car still have its original spark plugs? If so it is time to change them before looking elsewhere.

 

Aside for being more of an annoyance than anything, I don't think it's doing any harm. I've dealt with the idle issue for as long as I can remember... even back when I bought my 03 MCS with 36k miles in 2005. Hell, I actually recall a time when my MINI stalled out when the idle got rough and I didn't blip the throttle like I usually do to smooth things out. I keep hearing that it's a glitch in the software, but I'm not sure if any head way has been made to actually pinpoint the problem.

GotMINI

 

Now i have a different problem and the sound is hard to describe like screeching+metallic noises, ill give details if it comes back though. But thanks for your input guys as i havent experienced the rough idle since i got back the car from the dealer. maybe its fixed with a new radiator or because i fueled up at a different shell station. hopefully it doesnt come back (crosses fingers).