There's not much in the logs to draw any conclusion. That notice is nothing serious and will be fixed in the next update, but I am really without ideas what is wrong in your system.
Try to re-upload all files manually again to your server and see if that helps. Also, stick with default Bender theme for a while, until you get it fixed.
There are no changes that should break things like this (that I am aware of) in the new version, unless your problem is related to MySQL 5.7 somehow. Check your queries logs, as well. Look for ERROR keywords.
How does your old version (3.6.1) work on MySQL 5.7? Because, it cannot work properly, 3.6.1 does not support new MySQL version. This is the first mystery about your entire setup, you give very little useful information from the start.