If this is the case, it might be best to update the plugin listing. It currently states that the requirement is “Requires PHP Version: 5.2.4 or higher” which is misleading.
Similar issue on two of my sites. However, I have found that if I use the Settings->Discussion Page to set the contents of the blacklist, it can be restored correctly. If I try to use the list in Tools-Ban Hammer, I lose a significant part of the list when I save the update.