That helped me find the cause for some reason.

I have found a ticket for an improvement for version 9 TL-10429 that explains what is happening.

The 'Process messages and alerts'  task automatically dismisses messages after 30 days. To prevent this in the scheduled task disable this task - this will mean the file will keep growing but should be manageable..

Version 9 has renamed this task to 'Dismiss alerts and tasks after 30 days' and created a separate task to cleanup messaging related data so this can be run when required.