unaligned partitions

You can make parted list the partition table in units of sectors,
then ensure that (assuming 512-byte sectors) each partition's
start sector is divisible by some round number, like 2048
if you want them to be 1MiB-aligned.

For example, here all partitions are MiB-aligned, except
for the first one, which is only 32KiB-aligned. But since it's
only for grub, that is ok:

$ parted -m -s -- /dev/sdb u s p free
BYT;
/dev/sdb:117231408s:scsi:512:512:gpt:ATA OCZ-VERTEX2;
1:34s:63s:30s:free;
1:64s:4095s:4032s:ext2:_grub_bios:bios_grub;
2:4096s:1048575s:1044480s:ext3:_/boot:boot;
3:1048576s:12582911s:11534336s:ext4:_/:;
4:12582912s:16777215s:4194304s:linux-swap(v1):_/swap:;
5:16777216s:37748735s:20971520s:ext4:_/usr:;
6:37748736s:52428799s:14680064s:ext4:_/var:;
7:52428800s:52449279s:20480s:ext4:_/full:;
8:52449280s:117229567s:64780288s:ext4:_/h:;
1:117229568s:117231374s:1807s:free;

Please do not use parted's "move" command. It is risky since it tries
to be smart and is file-system aware. In addition to moving the partition
it may try to move an embedded file system, too, but its built-in FS-aware
code is so old and unreliable that it is slated to be removed altogether.

If you try to use that sub-command (or e.g., mkpartfs which is in the same
boat), recent versions of parted will emit a big warning telling you some
of the above.