I'm not spotting anything immediately obvious that would cause this problem... but I guess the core issue is that Thinking Sphinx, within the context of cron, doesn't think that Sphinx is running. The fact that it's not consistent with this is definitely confusing.
Can you run us through the contents of your sphinx.yml file, if you have one?
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Pat
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Permissions could have certainly played a part in why things wouldn't work... but still, if you hit any further problems, let us know.
Cheers
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Pat
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