I have a Moodle 1.9.7, 1.9.8 and 1.9.9 site and on them you can tell Statistics how far back the logs should be processed the first time. By default it is not turned on to limit how far back it starts. Check it and you might be able to to change it and get your system off it's knees.
Teaching with Moodle
Monitoring student progress
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