Missing wp_usermeta and wp_posts MYD/MYI data files with recent WP versions

A bit of a strange one here, arguably this is more of an SQL question, but I can’t help believe it’s linked to more recent versions of WordPress.

I have many WP sites, all working fine. However, following a server crash and rebuild, I noticed that a few of my WP sites had incomplete MySQL data files:
– wp_posts.MYD and wp_posts.MYI
– wp_usermeta.MYD and wp_usermeta.MYI
the .frm files for both tables are however present.

The issue wasn’t really apparent before the crash: the sites were working fine because of the MySQL data files (ibdata1, ib_logile0 and ib_logfile1). WP was retrieving/using the table data held in those files.

I have now been able to recover the ibdata1 and logfiles, and, having restored them, the sites with the missing MYD and MYI files are operational once more. However, I’d like to have a complete set of files, not ones which also rely on the huge common ibdata1 file.

The reason why I’m wondering whether this is WP-relate is because I’ve now noticed this on 3 different WP installations. All 3 have the same missing files from the same tablenames. And all 3 were recent installations of WP.

If this isn’t a WP-related issue, maybe it’s a MySQL “feature”? I can’t remember, but maybe there had been a minor revision of MySQL installed between my earlier WP sites which have full sets of data files and the 3 which have the missing data files.

Using phpMyadmin, I’ve made a copy of a problematic WP database, selecting structure and data, but the backup copy still has the missing data files…

I’ve also made an .sql backup, but not sure if this will have the missing tables as well :/

Any ideas on how to recreate the data tables fully?

Server details:
Ubuntu 14.04 LTS
MySQL 5.5.40
PHP 5.5.9