Copy & past from upstream:

     # modprobe scsi_debug dev_size_mb=1024 sector_size=4096
    
     # fdisk /dev/sdb
    
      Command (m for help): n
      Command action
        e   extended
        p   primary partition (1-4)
      p
      Partition number (1-4, default 1):
      Using default value 1
      First sector (256-262143, default 256): 257
      Last sector, +sectors or +size{K,M,G} (257-262143, default 262143): +100M
    
      Command (m for help): p
    
      Disk /dev/sdb: 1073 MB, 1073741824 bytes
      32 heads, 32 sectors/track, 256 cylinders, total 262144 sectors
      Units = sectors of 1 * 4096 = 4096 bytes
      Sector size (logical/physical): 4096 bytes / 4096 bytes
      I/O size (minimum/optimal): 4096 bytes / 262144 bytes
      Disk identifier: 0x16db2bb0
    
        Device Boot      Start         End      Blocks   Id  System
      /dev/sdb1            257       25855      102396   83  Linux
      Partition 1 does not start on physical sector boundary.
      ^^^^^^^^
    
     The warning is nonsense. The logical and physical sector size is the
     same. It means that every LBA is always aligned to physical sector
     boundary.
    
     Note that this bug does not mean that fdisk produces unaligned
     partitions. The problem is that fdisk forces to use bigger gaps
     between aligned LBAs, for example:
    
       correctly aligned LBA are: 256, 257, 258, ...  [N+1]
       fdisk assumes:             256, 264, 272, ...  [N+(sector_size/512)]
    

Bug fix is pretty simple:

-	unsigned long long offset = (lba << 9) & (granularity - 1);
+	unsigned long long offset = (lba * sector_size) & (granularity - 1);