This happened when I deleted my old Ubuntu partition and re-installed a newer version of Ubuntu. Even though there was a logical swap partition present, Ubuntu simply ignored it and created its own swap file. A glance through the Swap FAQ showed me how to fix it.
First, you need to have a look at what the UUID of your swap partition is. Do that by running:
blkid
Search for the line containing TYPE="swap", and note the UUID at the start of the line. This is the UUID of the swap partition. For example, the UUID may be fdb91fbe-e580-467f-8819-b672d89261eb.
Now open up fstab.
sudo gedit /etc/fstab
If there's a line starting with "/swapfile", comment out that line using a hash at the start of the line "#/swapfile". This is the swapfile that Ubuntu used instead of using the swap partition you had created.
Now add a new line to the file, where you mention the UUID that Ubuntu can use to recognize the swap partition:
UUID=fdb91fbe-e580-467f-8819-b672d89261eb none swap sw 0 0
Save and exit. Reboot.
Voila! The swap partition will now be recognized.
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