I do not think you have an issue unless you use an old (over 2years old) copy of gparted or the installer. Also if you encrypt /home then gparted will not see swap as swap is also encrypted.
Since drives became over 8GB CHS cylinders, heads, sectors has been obsolete and LBA is how drive is configured. For more compatibility with newer drives, 4k drives, SSDs and better configuration, partitions now start at sector 2048 rather than rounding to cylinders. With 512 bytes per sector that is 1MB at the beginning of the drive.
http://en.wikipedia.org/wiki/Cylinder-head-sector
First, understand that most partitioning tools have moved to a policy of aligning partitions on 1 MiB (2048-sector) boundaries as a way of improving performance with some types of arrays and some types of new hard disks (those with 4096-byte physical sectors). See article by srs5694:
http://www.ibm.com/developerworks/li...-sector-disks/
Post on 8-sector boundaries alignment by srs5694
http://ubuntuforums.org/showthread.php?t=1685666
it's 8-sector (4096-byte) alignment
http://ubuntuforums.org/showthread.php?t=1768635
Alignment issues on 4K drives
http://ubuntuforums.org/showthread.php?t=1635018
srs's to show 8 sector alignment
$ sudo parted /dev/sda unit s print
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