Comment 4 for bug 1506139

I tried to reproduce this on today's ubuntu desktop amd64 image (20151014). I think I set up partitions like you described: 1 GB /boot on partition 1, 1 GB LUKS on partition 2 (and put swap on vda2_crypt), 8 GB LUKS on partition 3 (and put btrfs / on vda3_crypt).

Both during install and after a few reboots I see correct partition/file system types in "blkid":
$ blkid
/dev/mapper/vda3_crypt: UUID="5d281986-88e6-4a51-97a3-72f7af49792a" UUID_SUB="f31e41da-5fb9-401e-82c6-c8ba0fc031a6" TYPE="btrfs"
/dev/mapper/vda2_crypt: UUID="1fda8cc2-08b8-4c2c-820a-7ac07014ab3b" TYPE="swap"
/dev/vda1: UUID="947e51a6-196c-40f9-a9fe-9a53429bbaaa" TYPE="ext4" PARTUUID="1d8c299a-01"
/dev/vda2: UUID="7a5a8534-53ca-4cf9-ae69-3d164c9d7ab6" TYPE="crypto_LUKS" PARTUUID="1d8c299a-02"
/dev/vda3: UUID="aa700da9-6f7e-4de9-ae1d-3db0988dd0fe" TYPE="crypto_LUKS" PARTUUID="1d8c299a-03"

The only change was in the UUID of vda2_crypt as that gets re-mkswap-ed every time due to the "swap" option in crypttab. If that's undesired, this needs to be fixed in partman -- however, it doesn't sound like that's the actual issue you see.

My /etc/crypttab looks pretty much like your's:
vda2_crypt UUID=7a5a8534-53ca-4cf9-ae69-3d164c9d7ab6 none luks,swap,discard
vda3_crypt UUID=aa700da9-6f7e-4de9-ae1d-3db0988dd0fe none luks,discard

and /etc/fstab isn't surprising either:
dev/mapper/vda3_crypt / btrfs defaults,subvol=@ 0 1
# /boot was on /dev/vda1 during installation
UUID=947e51a6-196c-40f9-a9fe-9a53429bbaaa /boot ext4 defaults 0 2
/dev/mapper/vda3_crypt /home btrfs defaults,subvol=@home 0 2
/dev/mapper/vda2_crypt none swap sw 0 0

So I can't reproduce "destroys swap partition" just yet. From your description it sounds like something is destroying sda3 itself (i. e. the outer encrypted LUKS partition), *not* the unencrypted sda3_crypt, right?

Can you please give me some details:

 - What do you precisely do to "repair the swap manually"?
 - After that, please copy&paste the output of "sudo blkid", "sudo swapon -s", "cat /etc/crypttab", and "cat /etc/fstab".
 - Reboot
 - After that, please copy&paste all of the above commands again, so that we can compare.
 - Run "sudo journalctl -b > /tmp/journal.txt" and attach /tmp/journal.txt as well.

Thanks!