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I am also having this same problem with FreeBSD 6.2 and Sympa 5.2.4.

The probe_db routine isn't recognizing that the tables already exist.
Furthermore, it is sending invalid SQL to the server. In particular:

SHOW FIELDS FROM sympa`.`admin_table

The settings in my sympa.conf file are correct. If I empty the database, the
first run of Sympa creates the tables and populates them with data it gathers
from the SYMPA/expl directories. However, on subsequent runs, it attempts to
create the tables again and fails due to the wrong SQL (above).