I happened to stumble upon this problem for 3 different releases of Ubuntu on two different computers. While most of the time the swap-partition was mounted despite the warning message, sometimes the GUI refused to start upon boot completion because of it.

Here's what I did as a workaround:

Open a terminal by pressing Ctrl + Alt + T.

Type gksudo gedit /etc/fstab and press Enter.

Search for the line that reads:

/dev/mapper/cryptswap1 none swap sw 0 0

Now enter the value noauto right after sw (separated by a comma), so it looks like this:

/dev/mapper/cryptswap1 none swap sw,noauto 0 0

Save and exit. This way, your swap partition won't be mounted while booting, thus the warning message won't appear or even hinder the login screen to appear.

Now type in a terminal

gksudo gedit /etc/rc.local

and enter the following lines before the entry exit 0:

sleep 10

swapon /dev/mapper/cryptswap1

If there's no entry exit 0, you'll have to enter it right beneath those two lines.
Save and exit again. This will tell your system to wait 10 seconds after login to mount your encrypted swap partition.

Reboot your system. You should not get the warning message any longer. After login, wait some time, then open up a terminal again and type

free -m

Your output should look something like this:

fuzzyq@Samsung-R710:~$ free -m

              total       used       free     shared    buffers     cached



 Mem:          3949       3806        143          0         86       1783



 -/+ buffers/cache:       1936       2013



 Swap:         4095          0       4095

The last line is the important one. If there's a positive value showing for total swap, your swap partition was being mounted successfully.