It appears that if you upgrade to Workbench 6.0 in order to run db backups, that it doesn't work..
I've found some comments about how PHP uses a 41-byte password now instead of the 16-byte password since MySQL 4.1.
And, if you try to use Workbench 6.0 on your Threads database, it won't recognize the password.
Has anyone else run into this, or have a suggestion?