A Power Commander won't affect the warranty. Read 'shouldn't'!
You don't say what year your 12 is.
First, has it got the later airbox and ICV? If not, get the kit from BMW. Pricy but it fixed mine, along with the associated ECU re-flash. After this update my PC, which was fitted immediately prior to finding out about the mods, was redundant.
Second, if it has have you tried removing, cleaning and re-setting the ICV? If not, do that next.
Mine was never perfect but it got rid of the low-speed, low-rev jerkiness.
PM Martin (fjtwelve) for details of his re-map and the amazing results.