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Yes.
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As Pieter said, they don't count towards your wallet balance because you don't have ALL of the private keys in your wallet.
It is not clear which wallet those 1-of-2 coins belong to, since neither has exclusive control over them. So the code is conservative and doesn't add them to your balance unless you have ALL of the private keys.
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The 0.7 release will have a set of RPC calls to create and sign transactions that spend from multisig inputs: see https://gist.github.com/2839617