Try something like this:
$authAdapter->setTableName('USER_TABLE')
->setIdentityColumn(new Zend_Db_Expr('LOWER(USERID)'))
->setCredentialColumn('PASSWORD');
The problem is that if you pass 'LOWER(USERID)' as a simple string, Zend will put quotes around it, causing it to create an invalid query. Using Zend_Db_Expr will stop Zend doing this.