After a fresh install of 4.2.0d Pro I've run Repair Database, option Display SQL and I've got:

/* Table : files */
/*COLUMNS/*
/*MISMATCH WITH DATABASE - id - ROW [Field] => 'id' [Type] => 'char(36)' [Null] => 'NO' [Key] => 'PRI' [Default] => '' [Extra] => '' */
/* VARDEF - id - ROW[Field] => 'id' [Type] => 'varchar(36)' [Null] => 'NO' [Key] => 'PRI' [Default] => '' [Extra] => '' */
alter table files modify column id varchar(36) NOT NULL
/*MISMATCH WITH DATABASE - assigned_user_id - ROW [Field] => 'assigned_user_id' [Type] => 'char(36)' [Null] => 'YES' [Key] => 'MUL' [Default] => '' [Extra] => '' */
/* VARDEF - assigned_user_id - ROW[Field] => 'assigned_user_id' [Type] => 'varchar(36)' [Null] => 'YES' [Key] => 'MUL' [Default] => '' [Extra] => '' */
alter table files modify column assigned_user_id varchar(36)
/*INDEXES/*
/* Table : team_memberships */
/*COLUMNS/*
/*MISMATCH WITH DATABASE - id - ROW [Field] => 'id' [Type] => 'char(36)' [Null] => 'NO' [Key] => 'PRI' [Default] => '' [Extra] => '' */
/* VARDEF - id - ROW[Field] => 'id' [Type] => 'varchar(36)' [Null] => 'NO' [Key] => 'PRI' [Default] => '' [Extra] => '' */
alter table team_memberships modify column id varchar(36) NOT NULL
/*MISMATCH WITH DATABASE - team_id - ROW [Field] => 'team_id' [Type] => 'char(36)' [Null] => 'YES' [Key] => 'MUL' [Default] => '' [Extra] => '' */
/* VARDEF - team_id - ROW[Field] => 'team_id' [Type] => 'varchar(36)' [Null] => 'YES' [Key] => 'MUL' [Default] => '' [Extra] => '' */
alter table team_memberships modify column team_id varchar(36)
/*MISMATCH WITH DATABASE - user_id - ROW [Field] => 'user_id' [Type] => 'char(36)' [Null] => 'YES' [Key] => 'MUL' [Default] => '' [Extra] => '' */
/* VARDEF - user_id - ROW[Field] => 'user_id' [Type] => 'varchar(36)' [Null] => 'NO' [Key] => 'MUL' [Default] => '' [Extra] => '' */
alter table team_memberships modify column user_id varchar(36) NOT NULL
/*MISMATCH WITH DATABASE - date_modified - ROW [Field] => 'date_modified' [Type] => 'datetime' [Null] => 'NO' [Key] => '' [Default] => '' [Extra] => '' */
/* VARDEF - date_modified - ROW[Field] => 'date_modified' [Type] => 'datetime' [Null] => 'YES' [Key] => '' [Default] => '' [Extra] => '' */
alter table team_memberships modify column date_modified datetime
/*MISMATCH WITH DATABASE - deleted - ROW [Field] => 'deleted' [Type] => 'tinyint(1)' [Null] => 'YES' [Key] => '' [Default] => '0' [Extra] => '' */
/* VARDEF - deleted - ROW[Field] => 'deleted' [Type] => 'tinyint(1)' [Null] => 'NO' [Key] => '' [Default] => '0' [Extra] => '' */
alter table team_memberships modify column deleted bool DEFAULT '0' NOT NULL
/*INDEXES/*
/*INDEX MISMATCH WITH DATABASE - idx_teammemb_team_user - ROW [Table] => 'team_memberships' [Non_unique] => '1' [Key_name] => 'idx_teammemb_team_user' [Seq_in_index] => '2' [Column_name] => 'user_id' [Collation] => 'A' [Cardinality] => '4' [Sub_part] => '' [Packed] => '' [Null] => 'YES' [Index_type] => 'BTREE' [Comment] => '' */
/* VARDEF - idx_teammemb_team_user - ROW[Table] => 'repair_table' [Non_unique] => '1' [Key_name] => 'idx_teammemb_team_user' [Seq_in_index] => '2' [Column_name] => 'user_id' [Collation] => 'A' [Cardinality] => '0' [Sub_part] => '' [Packed] => '' [Null] => '' [Index_type] => 'BTREE' [Comment] => '' */
ALTER TABLE team_memberships DROP INDEX idx_teammemb_team_user
ALTER TABLE team_memberships ADD INDEX idx_teammemb_team_user (team_id, user_id)


After a fresh install of 4.2.1a Pro and running the same Repair Database, option Display SQL I've got:

/* Table : files */
/*COLUMNS/*
/*MISMATCH WITH DATABASE - id - ROW [Field] => 'id' [Type] => 'char(36)' [Null] => 'NO' [Key] => 'PRI' [Default] => '' [Extra] => '' */
/* VARDEF - id - ROW[Field] => 'id' [Type] => 'varchar(36)' [Null] => 'NO' [Key] => 'PRI' [Default] => '' [Extra] => '' */
alter table files modify column id varchar(36) NOT NULL
/*MISSING IN DATABASE - date_modified - ROW/*
alter table files add column date_modified datetime
/*MISMATCH WITH DATABASE - assigned_user_id - ROW [Field] => 'assigned_user_id' [Type] => 'char(36)' [Null] => 'YES' [Key] => '' [Default] => '' [Extra] => '' */
/* VARDEF - assigned_user_id - ROW[Field] => 'assigned_user_id' [Type] => 'varchar(36)' [Null] => 'YES' [Key] => 'MUL' [Default] => '' [Extra] => '' */
alter table files modify column assigned_user_id varchar(36)
/*INDEXES/*
/*MISSING INDEX IN DATABASE - idx_cont_owner_id_and_name -index ROW/*
ALTER TABLE files ADD INDEX idx_cont_owner_id_and_name (assigned_user_id, name, deleted)
/* Table : team_memberships */
/*COLUMNS/*
/*MISMATCH WITH DATABASE - id - ROW [Field] => 'id' [Type] => 'char(36)' [Null] => 'NO' [Key] => 'PRI' [Default] => '' [Extra] => '' */
/* VARDEF - id - ROW[Field] => 'id' [Type] => 'varchar(36)' [Null] => 'NO' [Key] => 'PRI' [Default] => '' [Extra] => '' */
alter table team_memberships modify column id varchar(36) NOT NULL
/*MISMATCH WITH DATABASE - team_id - ROW [Field] => 'team_id' [Type] => 'char(36)' [Null] => 'YES' [Key] => 'MUL' [Default] => '' [Extra] => '' */
/* VARDEF - team_id - ROW[Field] => 'team_id' [Type] => 'varchar(36)' [Null] => 'YES' [Key] => 'MUL' [Default] => '' [Extra] => '' */
alter table team_memberships modify column team_id varchar(36)
/*MISMATCH WITH DATABASE - user_id - ROW [Field] => 'user_id' [Type] => 'char(36)' [Null] => 'YES' [Key] => 'MUL' [Default] => '' [Extra] => '' */
/* VARDEF - user_id - ROW[Field] => 'user_id' [Type] => 'varchar(36)' [Null] => 'NO' [Key] => 'MUL' [Default] => '' [Extra] => '' */
alter table team_memberships modify column user_id varchar(36) NOT NULL
/*MISMATCH WITH DATABASE - date_modified - ROW [Field] => 'date_modified' [Type] => 'datetime' [Null] => 'NO' [Key] => '' [Default] => '' [Extra] => '' */
/* VARDEF - date_modified - ROW[Field] => 'date_modified' [Type] => 'datetime' [Null] => 'YES' [Key] => '' [Default] => '' [Extra] => '' */
alter table team_memberships modify column date_modified datetime
/*MISMATCH WITH DATABASE - deleted - ROW [Field] => 'deleted' [Type] => 'tinyint(1)' [Null] => 'YES' [Key] => '' [Default] => '0' [Extra] => '' */
/* VARDEF - deleted - ROW[Field] => 'deleted' [Type] => 'tinyint(1)' [Null] => 'NO' [Key] => '' [Default] => '0' [Extra] => '' */
alter table team_memberships modify column deleted bool DEFAULT '0' NOT NULL
/*INDEXES/*
/*INDEX MISMATCH WITH DATABASE - idx_teammemb_team_user - ROW [Table] => 'team_memberships' [Non_unique] => '1' [Key_name] => 'idx_teammemb_team_user' [Seq_in_index] => '2' [Column_name] => 'user_id' [Collation] => 'A' [Cardinality] => '2' [Sub_part] => '' [Packed] => '' [Null] => 'YES' [Index_type] => 'BTREE' [Comment] => '' */
/* VARDEF - idx_teammemb_team_user - ROW[Table] => 'repair_table' [Non_unique] => '1' [Key_name] => 'idx_teammemb_team_user' [Seq_in_index] => '2' [Column_name] => 'user_id' [Collation] => 'A' [Cardinality] => '0' [Sub_part] => '' [Packed] => '' [Null] => '' [Index_type] => 'BTREE' [Comment] => '' */
ALTER TABLE team_memberships DROP INDEX idx_teammemb_team_user
ALTER TABLE team_memberships ADD INDEX idx_teammemb_team_user (team_id, user_id)
/* Table : acl_roles_actions */
/*COLUMNS/*
/*INDEXES/*
/*MISSING INDEX IN DATABASE - idx_aclactions_roles -index ROW/*
ALTER TABLE acl_roles_actions ADD

PHP 4.4.2
MySQL 5
IIS 5
W2K Server

SugarCRM's support team told me:
...it may be a bug as such, but the general consensus is that these error messages are not harmful.

My questions:
- could someone try this and let know how it goes?
- why does this occur?
- if this is not harmful, how can I make the difference to a harmful one?
- wouldn't be better to have this fixed and an empty output for a healthy system, in order to better identify the real trouble?

George