I took a look at my own blog's mt.cfg file, and I don't even have that line commented out.
Perhaps you don't have the MySQL settings set correctly in mt.cfg, so MT is assuming you want to use Berkeley DB. I'm also guessing that if it doesn't find the DataSource setting in mt.cfg, it attempts to use the default value of ./db. This is just a guess; I haven't looked at the actual code.
You've probably already done this, but check again to make sure the following settings are correct for your installation.
Settings for MySQL
Database Name of your database
DBUser Valid username for your database
DBHost domain associated with your database
The first setting is crucial. Capitalization matters.
Then, go to the MySQL section of the control panel.
Find the database you created for MT. Make sure the database name exactly matches the value above in mt.cfg for Database.
Directly below the name of your database should be a table (an HTML one) where the first column is titled "Service Type". There should be at least one row with an icon meant to represent a user. The value under the "Setting" column is the name of the user. Make sure this name exactly matches what you have entered for DBUser.
There should also be a row with an icon meant to represent a server. The setting is the domain name associated with your database. Make sure the value exactly matches what you have entered for the DBHost setting.