I recently installed Ubuntu on a SSD with logical/physical sector size 
of 4096/4096.  Everything works fine; however, just for curiosity I did 
a check on the efi partition 500MB, formatted as FAT32.

I got the following error messages: (See image).

This does not happen on a usb drive with 512 byte sectors.

Everything looks fine when I check with fsck.fat:

fsck.fat 4.1 (2017-01-24)
Checking we can access the last sector of the filesystem
Boot sector contents:
System ID "mkfs.fat"
Media byte 0xf8 (hard disk)
       4096 bytes per logical sector
       4096 bytes per cluster
         32 reserved sectors
First FAT starts at byte 131072 (sector 32)
          2 FATs, 32 bit entries
     512000 bytes per FAT (= 125 sectors)
Root directory start at cluster 2 (arbitrary size)
Data area starts at byte 1155072 (sector 282)
     127718 data clusters (523132928 bytes)
63 sectors/track, 255 heads
       2048 hidden sectors
     128000 sectors total
Checking for unused clusters.
Checking free cluster summary.
/dev/sda1: 11 files, 1997/127718 clusters


Here is the output you requested from parted:


Model: Unknown (unknown)
Disk /dev/sda1: 524MB
Sector size (logical/physical): 4096B/4096B
Partition Table: loop
Disk Flags:

Number  Start  End    Size   File system  Flags
  1      0.00B  524MB  524MB  fat32

Model: Unknown (unknown)
Disk /dev/sda1: 128000s
Sector size (logical/physical): 4096B/4096B
Partition Table: loop
Disk Flags:

Number  Start  End      Size     File system  Flags
  1      0s     127999s  128000s  fat32

Model: Unknown (unknown)
Disk /dev/sda1: 55,197,1
Sector size (logical/physical): 4096B/4096B
BIOS cylinder,head,sector geometry: 55,255,9.  Each cylinder is 9400kB.
Partition Table: loop
Disk Flags:

Thanks!

Eric (Wood)