IsPersistent not working - Cookie only valid for current session

This is a known bug in Identity and by looking on this answer it is not very new.

When cookie is regenerated on every request, "IsPersisted" flag is not set, when, even when it was set in the original cookie.

To work around this, you will need to implement your own version of cookie validator that will set the flag as is should.

I think I've got the solution for you, but I have not compiled or tested it - just merely a general direction of where you need to go. See this gist for full code.
This is just a SecurityStampValidator code taken from decompiler. I've added lines 91-96. Basically I take "IsPersistent" flag from the previous cookie and add it to the new cookie, when it is created. That was not done in non-modified version.

And then in your Auth.Config you do:

Provider = new CookieAuthenticationProvider
            {
                OnValidateIdentity = MySecurityStampValidator.OnValidateIdentity(
                    validateInterval: TimeSpan.FromMinutes(0),
                    regenerateIdentity: (manager, user) => user.GenerateUserIdentityAsync(manager))
            }

Beware though, when new version is out, check if this was fixed, so you can remove the dirty fix. This issue is reported to be fixed, but shortly after v2.1 was out.