Hi inception,
As in change logs, we have moved the menu configuration to database instead of using ini setting file.
So the first trouble will be a known issue.
For the problem that you can not save changes of menu configuration, it is really weird.
I does not have the same problem as yours.
Have you upgrade both template and plugin or just plugin only.
Please download the latest package on https://github.com/t3framework/t3/tags Source code (zip) file
Then goto Extension Manager of Joomla and install the whole package. (You do not have to separate plugin and template package, just install the zip file).
Please check again if you still have problem.
And please provide some information about your site (ftp/admin) so that I can help you and we can help to improve T3.
Regards