I have not looked at 7.x but I wonder if there is still a issue in apps/base/libraries/System.php. In 6.x it is calling the command "shutdown -t3 -r now" and I posted on the issue a couple of years ago but got nowhere. If you have a "-t" I don't think you should have "now" as they conflict. Also there may need to be a space between the "t" and the "3". I'll need to test on a VM as I can't check on the live box. Unfortunately I have a feeling this may be hardware dependant otherwise lots of people would have reported it.

Yes,

halt -p also works (but leaves putty hanging)

Someone who knows what script we have to change so the webconfig "halt" script works?

I had the same issue with either 5.x or 6.x with the webconfig and never cracked it. I now always shut it down from the console or the command line - either:

shutdown -h now

(a bit brutal and leaves PuTTy hanging)

or

shutdown -h -t 1 && exit

(shuts PuTTy down nicely)

I have not tried the webconfig recently.