Unfortunately, we don't (yet) have the ability to leave a folder "untouched" on a volume. As such, when you ignore the .Spotlight... folder, it ends up being removed.
This whole area of Spotlight is annoying, and we're trying to come up with ways of handling it. (We've also filed bugs against it.) Our disable_spotlight script -- which uses mdutil -- does turn the indexing off for the volume, but it's still searched... and whatever the privacy tab is doing is not documented, so we don't want to "hack" it in there...
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--Dave Nanian
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