Looks like you just fixed it yourself! That’s good to know.
For anyone else reading this: There was a bug which was introduced shortly after v2.6.0.beta1. I fixed it in https://github.com/discourse/discourse/commit/f51ccea02816c768863b1073977db219f4b66ff3 and backported it to the beta branch.
From now on backups will be created correctly again and restoring a backup that was created in the time between v2.6.0.beta1 and the bugfix will work as well.