The index is only for when multi-lang-content is on. The fix is for the repair tool to be aware of that (EDIT: I think, although I saw you made a different fix since).

Creation is skipped via this code:
if (($is_full_text) && (multi_lang_content()) && (strpos($db_type, '_TRANS') !== false)) {
return null; // We don't create a full-text index on *_TRANS fields if we are directing through the translate table
}

Actually the solution was different. This occurred during the enable content translation script because the script was altering the database columns before globally enabling multi lang content. As a result, the columns were just getting re-created as longtext when they should have been integer. So I had the script enable multi lang content before altering the database, and that resolved the issue.