While reloading a Cisco Catalyst 3560 running IOS 12.2(55)SE the other day, I noticed the switch stopped sending messages to the configured IPv6 enabled syslog host. Nothing appeared in the log files on the syslog host until I manually disabled and reenabled the log statement.
Please drop me a note if you have enabled logging to an IPv6 enabled syslog host with a statement such as
logging host ipv6 2001:db8:1:2::3
and are experiencing the same issue, or maybe you even have a solution.