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This might help you narrow it down. I'm running Mint 14 with Cinnamon 1.6 and a library with not one but two yes/no custom columns and I don't see the problem you're seeing.
Which makes me think it's either the changing of the icon size (combined with the above) or the removing of items from the toolbar (ditto).
I can play around with this tonight and see if I can reproduce your problem.
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