How to format a 4k sector hard drive?

How to format a 4k sector hard drive?

I bought a Seagate ST3000DM001 3TB hard drive. It was sold inside an
enclosure. I formatted to ext4, copied some data to it and then I removed
it from the enclosure and connected it directly to the motherboard. My
data wasn't visible to OS (it was seeing one unknown ~300GiB partition and
the rest as free space) so I started reading about Advanced Format and
>2TB drives.
I connected the disk with USB again, copied all the data, and plugged to
sata once again. I used gparted to create a GPT partition table (the
ubuntu disk utility wouldn't let me with Error synchronizing after initial
wipe: Timed out waiting for object (udisks-error-quark, 0), created one
big 3Tb Ext4 partition, left the default Align to value to MiB and
formatted.
Gparted shows the disk having 512k sectors which I know is not true1

while cat /sys/block/sdb/queue/physical_block_size reports 4096
I have found some reports that libparted has a problem with non-512k
sectors2 and others3 that say that aligning to MiB is enough.
Parted reports that the drive is aligned when I choose minimal:
(parted) align-check
alignment type(min/opt) [optimal]/minimal? min
Partition number? 1
1 aligned
(parted)
Is my configuration correct? Do I have performance penalty because the
disk is formatted with 512k sectors, is gParted reporting false values or
I have understood the whole thing wrong?
http://www.storagereview.com/seagate_barracuda_3tb_review_1tb_platters_st3000dm001
http://ubuntuforums.org/showthread.php?t=1536933&p=9754234#post9754234
http://wdc.custhelp.com/app/answers/detail/a_id/5655