If I am correct (and I am not 100% certain) only the permanent bans get written to listip.cfg. Other bans are just kept in the servers memory, and that memory is erased when your server crashes/shuts down.
You will need another ban plugin. Try for example exolent's Advanced Bans:
http://forums.alliedmods.net/showthread.php?t=80858
I have the same problem as you bytheway, but I am waiting for exolent to support SQL. Untill then I'll have to live with the problem.
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