the message is a bit of a red herring. Slackware 14.1 version of fdisk already defaults to the modern options of sector mode and non-dos mode for the partition table. If you create a first partition it will by default start at 2048 sector which is safe, as it is a multiple of 4kbytes (1MB). I had the same message which got me checking things, like you, only to find it was a false alarm.
If you format using ext4, then even if it wasn't aligned, it wouldn't make much speed difference. - see this report by ibm
for a table comparing different formats for unaligned partitions