Run into Live Mode using a Latest version of Ubuntu ISO or Gparted DVD. Later, while partitioning with "Gparted", when Gparted prompts for 1 MB left over space before the first Partition just allow it (This is the most Vital step.)

By default "Align to MiB" will be selected. Don't Change that. Do the rest of the partitioning normally. After you finish, to check whether the partitions are aligned properly; issue the following command on terminal:

sudo fdisk -l

If the output says /dev/sda1 start = 2048 and DOES NOT says "Partition X does not start on physical sector boundary." then you are good to go.

Another way is to use GPT partitioning scheme instead of MS-DOS. If you use GPT, then there is no special 1 MB free space allotment before the first partition is required. Gparted will make all the partitions 4k aligned by default.

For GPT Partitions:

To verify a partition is aligned, query it using /usr/bin/blockdev as
shown below, if a '0' is returned, the partition is aligned:

# blockdev --getalignoff /dev/<partition>

0