Hi @orangepizza,
This would certainly explain what happened with the system were certs were renewed in Nov 13 and where I started seeing the problem.
The strange thing however is that I had another system which had renewed certs in Oct 29 and which was working properly. I force renewed certs on this one and I got the short chain too :-?
Moreover upgrading to acme.sh 3.0.7 seems to have fixed the problem on both systems (after force renewing certs of course).
Strange...