Comme expliqué ici.

si vous passez à 5.1.12

Incompatible change: For utf8 columns, the full-text parser incorrectly considered several nonword 
punctuation and whitespace characters as word characters, causing some searches to return 
incorrect results. The fix involves a change to the full-text parser in MySQL 5.1.12, 
so as of 5.1.12, any tables that have FULLTEXT indexes on utf8 columns must be repaired with REPAIR TABLE:

REPAIR TABLE tbl_name QUICK;

Si vous passez à 5.1.16

Il sera nécéssaire de réindexer les fulltext

Incompatible change: The structure of FULLTEXT indexes 
has been changed in MySQL 5.1.6. After upgrading to 
MySQL 5.1.6 or greater, any tables that have FULLTEXT 
indexes must be repaired with REPAIR TABLE:

REPAIR TABLE tbl_name QUICK;

Comment trouver facilement ces tables ?

 SELECT `TABLE_NAME` FROM `STATISTICS` WHERE `INDEX_TYPE`= 'FULLTEXT' ;