I had a similar problem on my site with a custom cron job I wrote. It would run fine if I hit the Run button in the Admin CP, but it wouldn't run on it's own as a scheduled task. It was something to do with no longer being able to define any variable as global - I had to actually make sure every variable I used in my function was passed. I'm not sure if that is a problem at all with your functions. I don't remember if this happened after my server move or after my upgrade to 3.6.8.
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