I used gparted to create the partitions, which defaults to using MiB alignment rather than cylinder alignment. I used the defaults.
All partitions are ext4 except the data (videos) partition, which is xfs.
/dev/sda1 /boot (ext4)
/dev/sda3 /home (ext4)
/dev/sda5 /usr/local (ext4)
/dev/sda6 /tmp (ext4)
/dev/sda7 /var (ext4)
/dev/sda8 / (ext4)
/dev/sda9 data (xfs)
After creating the partitions on the new drive I copied the files from the old drive to the new drive. I did not use dd because I wanted to increase some of the partition sizes on the newer, larger drive and perform some nominal file/directory tweaking. I performed the updates using partedmagic. The entire operation was fast except copying files from the data partition, because many of the files are large video files.
I haven't noticed any other problem with the new drive. To have only one app behave oddly is a head scratcher. The xbmc files are on an ext4 partition (sda8).
/dev/sda8 / ext4 defaults,noatime 0 1
All partitions are using a 4096 block size, except sda1 (/boot), which is a small 128M partition and uses a 1024 block size:
tune2fs -l /dev/sdaX | grep "Block size"
Block size: 4096
fdisk does not complain about sector boundaries:
fdisk -lu /dev/sda
Disk /dev/sda: 1000.2 GB, 1000204886016 bytes
255 heads, 63 sectors/track, 121601 cylinders, total 1953525168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disk identifier: 0x0006861b
Device Boot Start End Blocks Id System
/dev/sda1 2048 264191 131072 83 Linux
/dev/sda2 264192 2361343 1048576 82 Linux swap
/dev/sda3 2361344 44304383 20971520 83 Linux
/dev/sda4 44304384 1953523711 954609664 5 Extended
/dev/sda5 44306432 46403583 1048576 83 Linux
/dev/sda6 46405632 48502783 1048576 83 Linux
/dev/sda7 48504832 50601983 1048576 83 Linux
/dev/sda8 50604032 79964159 14680064 83 Linux
/dev/sda9 79966208 1953523711 936778752 83 Linux
The block size on the older drive is also 4096.
Please explain why sector boundaries would cause such an anomaly.