>>Куда можно покопать?
>
>после обновления все порты пересобраны?

Да, делал по этому how-to http://druss.pp.ua/2009/12/обновление-freebsd-7-2-до-8-0/
MySQL не из портов ставился, а из инсталлятора DirectAdmina (после обновления пересобирался)

Добавил в /etc/mysql.conf
[mysql]
user = root
Начали повляться записи в логи

100129 11:07:12 mysqld_safe Starting mysqld daemon with databases from /usr/local/mysql/data
/usr/local/mysql-5.1.42-freebsd8.0-i386/bin/mysqld: Table 'mysql.plugin' doesn't exist
100129 11:07:12 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
Fatal error 'kse_create() failed
' at line 444 in file /usr/src/lib/libpthread/thread/thr_kern.c (errno = 2)
100129 11:07:12 mysqld_safe mysqld from pid file /usr/local/mysql/data/hostion.pid ended
100129 11:08:02 mysqld_safe Starting mysqld daemon with databases from /usr/local/mysql/data
/usr/local/mysql-5.1.42-freebsd8.0-i386/bin/mysqld: Table 'mysql.plugin' doesn't exist
100129 11:08:02 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
Fatal error 'kse_create() failed
' at line 444 in file /usr/src/lib/libpthread/thread/thr_kern.c (errno = 2)
100129 11:08:02 mysqld_safe mysqld from pid file /usr/local/mysql/data/hostion.pid ended

Запускаю mysql_upgrade, как рекомендуется:
#./mysql_upgrade
Looking for 'mysql' as: ./mysql
Looking for 'mysqlcheck' as: ./mysqlcheck
Running 'mysqlcheck with default connection arguments
./mysqlcheck: Got error: 2002: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (61) when trying to connect
FATAL ERROR: Upgrade failed

#./mysqlcheck -A -p
Enter password:
./mysqlcheck: Got error: 2002: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (61) when trying to connect

гуглим дальше про "Fatal error 'kse_create() failed")