I’ve made a FULLTEXT index on post_title,post_content,post_excerpt with no problem, that makes me think you’ve got a server configuration issue.
Version 3.1.3 installed all default tables as InnoDB which do not support fulltext.
I just installed a brand new, freshly downloaded WordPress 3.1.3 yesterday and the tables are all MyISAM. InnoDB is available on my SQL server so it could have been used if WP wanted it.
Interesting, i did installed it yesterday to, maybe you should just apply a db check and notice or ALTER function so nobody else assume the plugin is broken (it seems to be a popular plugin so many may encounter the same issue). InnoDB is mainly useful if WP uses commit, rollback and foreign keys, have not checked if it does. Percona mysql seems to build strict on InnoDB.
I’m not really in any position to “apply a db check” or anything else, as it isn’t my plugin.
Your problem has something to do with Percona? Is that what you mean?