Full text indexing not working + Mysql 5.6.4
You need check - configuration of server, memory for InnoDB, for FullText

compare size of index and FT buffer size, by default it only 8Mb, max value is 80Mb

Than next step and profile query - how many records returned, what time of intialyze of index

and upgrade 5.6.4 to something more new
in 5.6.4 FullText was only implement for InnoDB, many  bugs fixed from that time