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Do you know what transport is being used on the broken installations?

wp_remote_get() now uses the HTTP API library, which is supposed to try different ways of retrieving a remote HTTP resource. It is possible that the method the problem server is selecting to use looks like it is valid to WPMU but in fact isn’t for some configuration reason.

Beyond that I really can’t help without more specifics about your setup, mainly what transport method the HTTP API is using.