It just disappears... I've been told Server Armour may do this. Any idea why?

Same, and it's been happening since I believe the September update when FP switched the format of bans.cfg. The number at the end of each line used to be a UNIX timestamp (-1 for perm ban), and now each ban seems to have a unique ID as that number. I believe ServerArmor needs to be updated in order to stop wiping bans.cfg at every server start.

FWIW I'm running Linux server.

I have the same problem in my server!
Please you can fix that? The plug-in really helps the server. 

this is fixed now in 0.6.5

Thanks, the plug-in is great.

Thank you Pho3niX!