Я не наблюдаю эффекта ни с myisam, ни с innodb (версия сервера 5.0.45-community-nt MySQL Community Edition):
mysql> create table mytable(id bigint auto_increment primary key,name varchar(32) unique);
Query OK, 0 rows affected (0.01 sec)
mysql> insert ignore into mytable(name) values('aaa'),('bbb'),('ccc'),('aaa'),
mysql> ('ddd'),('eee'),('bbb'),('fff');
Query OK, 6 rows affected (0.02 sec)
Records: 8 Duplicates: 2 Warnings: 0
mysql> insert ignore into mytable(name) values('aaa'),('bbb'),('ccc'),('aaa'),
mysql> ('ddd'),('eee'),('bbb'),('ggg');
Query OK, 1 row affected (0.00 sec)
Records: 8 Duplicates: 7 Warnings: 0
mysql> select * from mytable;
+----+------+
| id | name |
+----+------+
| 1 | aaa |
| 2 | bbb |
| 3 | ccc |
| 4 | ddd |
| 5 | eee |
| 6 | fff |
| 7 | ggg |
+----+------+
7 rows in set (0.00 sec)
Аналогично при вставке из файла:
C:\>type test.txt
aaaa
bbbb
bbbb
cccc
dddd
bbbb
aaaa
eeee
mysql> create table mytable(id bigint auto_increment primary key,name varchar(32) unique);
Query OK, 0 rows affected (0.00 sec)
mysql> load data local infile 'c:\\test.txt' ignore into table mytable(name);
Query OK, 5 rows affected (0.00 sec)
Records: 8 Deleted: 0 Skipped: 3 Warnings: 0
mysql> select * from mytable;
+----+------+
| id | name |
+----+------+
| 1 | aaaa |
| 2 | bbbb |
| 3 | cccc |
| 4 | dddd |
| 5 | eeee |
+----+------+
5 rows in set (0.00 sec)
Какая у вас версия MySQL и как конкретно вы вставляете?