macOS Sierra boot problem related to Apple SD Card reader driver EDIT: It seems that upgrading to macOS 10.12.4 solved this issue. I had not have time to send the laptop to repair, as others did (and it fixed the issue for them). So far, restarting or shutdown / starting the OS no longer hangs the Filevault pre-boot screen.

--- ORIGINAL POST ---

After upgrading to El Capitan, and then to Sierra, I found a strange behaviour:


A - if I restart the os, it takes more time than usual, then I get into the boot screen with the input devices (keyboard, trackpad) responding from time to time (i.e. they work for 2 seconds, then they stop working for 10, then the cycle repeats itself);
B - during "A", I if I:


B1 - move the cursor to the "restart" button and press it, or force a shutdown - start by pressing the physical button, I get the os restarted in no time, and everything seems fine; BUT if I restart the os, I return to "A";
B2 - patiently try to type my password and enter the os, the mac starts normal;



Meanwhile, I was also experience SD Card problems - they wouldn't read at all or appear in Disk Utility; I now found out that if I do procedure B1 the SD Card reader seems not to work, but if I do procedure B2 it works ok.

I was almost sending the mac for hardware repair, but seems like there may be some problem with the SD Card reader drivers? I need to do some more testing, but meanwhile, has someone experienced this, or can give me some insight on how to debug this issue?

Using macbook Pro retina 2015 with macOS Sierra.

Thanks for you help.

EDIT: I did a clean install (completely formatted and partitioned the HD using a bootable USB stick with macOS Sierra on it). But it was for no avail, the problem persists.
I had the exact same issue. 2015 MacBook Pro 13", AppleCare. 

It took three attempts for the Apple service agent to resolve the issue, over the space of one month. 

The first time, they replaced the main logic board. 

The second time, they replaced the whole top case, including trackpad and battery. 

It was only after I found this post and brought it to their attention (including the fact that the SD card reader was showing as a fault when I ran system diagnostics) that on the third attempt they replaced the I/O board which contains the SD card reader and thankfully it worked.