2011 Mini Turn signal and power window problems
 

I have just changed the alternator on my Son's 2011 Mini Cooper Hatchback. When the original alternator failed he ran the car till the battery was dead. At that point I had the car towed home and I charged the battery back to full capacity. After checking the system I discovered that the Alternator had failed. I replaced it with a brand new 150 Amp unit and topped up the battery charge. When completed, the car started fine and everything to that point seemed normal. Upon further running through checks I discovered that the turn signals and the hazard flasher had stopped working as well as the interior lighting and power windows. Everything else to this point seems fine. Alternator is charging and battery is holding at just over 12 volts. I have put my OBD scanner on the vehicle and it is not throwing any codes back at me. I have checked all fuses and and have not found any blown. I also have not found any shorted relays. At this point I am at a loss. Any help would be greatly appreciated. Thanks

The battery should read 12.6 volts. I've seen bad batteries at 12.2 volts. Not that this is your issue, but does your sons R56 have an IBS unit? I suggest you read up on this article here: MINI Cooper R56 Battery and Connection Notes Replacement (2007-2011) | Pelican Parts DIY Maintenance Article. I also suggest you go to the bottom of that article and leave your comment there as well. Nick, our MINI guru will have additional input for you.