LP:949456 - MyISAM tables continuously crashing

I have a database with 13.000 tables on a dedicated MySQL server. Running MariaDB 5.2.10. I currently notice tables continuously crashing, syslog shows for such tables:
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Mar 7 22:45:20 mysql2 mysqld: 120307 22:45:20 [ERROR] mysqld: Incorrect key file for table './mx_messages/table_nl.MYI'; try to repair it
Mar 7 23:03:35 mysql2 mysqld: 120307 23:03:35 [ERROR] mysqld: Table './mx_messages/table_nl' is marked as crashed and should be repaired
Mar 7 23:03:35 mysql2 mysqld: 120307 23:03:35 [Warning] Checking table: './mx_messages/table_nl'
Mar 7 23:03:35 mysql2 mysqld: 120307 23:03:35 [Warning] Recovering table: './mx_messages/table_nl'
Mar 7 23:06:13 mysql2 mysqld: 120307 23:06:13 [Note] Found 5427 of 5541 rows when repairing './mx_messages/table_nl'
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I'm 100% sure the tables weren't corrupted earlier, because I did a full check/repair of all tables when things were not busy (I firewalled all external servers temporarily). We have around 20 servers writing to these tables at fast rate using REPLACE INTO. I'll upload the syslog, table structure, and part of the general log (private/confidential). This is on Debian Linux.