Apologies for the thread resurrection, but I'm having the exact same issue, and there doesn't appear to be any resolution to this; hence, I'm posting my information here.
Support Request Template
What version of phpBB are you using?
What is your board's URL? https://www.ron2k.za.net/forum/
Who do you host your board with?
Self-hosted, full root access. Server running the MySQL 5.6 package provided in the official Ubuntu 14.04 LTS repositories.
How did you install your board?
I used the download package from phpBB.com
What is the most recent action performed on your board?
Update from a previous version of phpBB3
Is registration required to reproduce this issue?
Do you have any MODs installed?
What version of phpBB3 did you update from?
What styles do you currently have installed?
Artodia: Deluxe Red
What language(s) is your board currently using?
Which database type/version are you using?
What is your level of experience?
Comfortable with PHP and phpBB
What username can be used to view this issue? No answer given
What password can be used to view this issue? No answer given
When did your problem begin?
Dropped mysql fulltext index, updated tables from MyISAM to InnoDB, attempted to recreate mysql fulltext index.
Please describe your problem.
SQL ERROR [ mysql4 ]
InnoDB presently supports one FULLTEXT index creation at a time 
ALTER TABLE phpbb3_posts MODIFY post_subject varchar(255) COLLATE utf8_unicode_ci DEFAULT '' NOT NULL, ADD FULLTEXT (post_subject), MODIFY post_text mediumtext COLLATE utf8_unicode_ci NOT NULL, ADD FULLTEXT (post_text), ADD FULLTEXT post_content (post_subject, post_text)
FILE: (not given by php)
LINE: (not given by php)
Issue persists after both mysqld and apache restarts.
Generated by SRT Generator
I've switched to fulltext native for the time being, but of course this isn't ideal.