Sorry you've had to do all this debugging on your own - but great to know you've found the cause.
I think this is actually a Rails/ActiveRecord bug, not a Thinking Sphinx bug (I've had someone raise it before) - as TS uses ActiveRecord to generate the joins in the sql_query.
So, I'm not sure if it's been fixed, but if you're not using 2.3.8, perhaps it's worth upgrading - at least temporarily - to check? Otherwise, I think manually editing the config and then using the ts:reindex task (to avoid config regeneration) is the only approach.
--
Pat
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Good to know the bug's fixed, too :)
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Pat