Same thing here, after the update to 4.0.20:
da1# mysql -V
mysql Ver 12.21 Distrib 4.0.14, for unknown-freebsd4.7 (i386)
and
da1# mysql -uroot -p
Enter password:
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 3 to server version: 4.0.14-standard
But I think I found the problem:
lrwxr-xr-x 1 root wheel 45 Apr 21 17:40 mysql -> mysql-standard-4.0.14-unknown-freebsd4.7-i386
After fixing this symlink, it seems to work a lot better:
da1# mysql -V
mysql Ver 12.22 Distrib 4.0.20, for unknown-freebsd4.7 (i386)