Protobuf has no terminator - so either close the stream, or use your own length prefix etc. Protobuf-net exposes this easily via SerializeWithLenghtPrefix / DeserializeWithLengthPrefix.
Simply: without this, it can't know where each message ends, so keeps trying to read to the end of the stream.
Sorry for taking a while to answer this. As Marc says, protocol buffers don't have a terminator, and they aren't length prefixed unless they're nested. However, you can put on the length prefix yourself. If you look at MessageStreamIterator and MessageStreamWriter, you'll see how I do this - basically I pretend that I'm in the middle of a message, writing a nested message as field 1. Unfortunately when reading the message, I have to use internal details (BuildImpl).
There's now another API to do this: IMessage.WriteDelimitedTo and IBuilder.MergeDelimitedFrom. This is probably what you want at the moment, but I seem to remember there's a slight issue with it in terms of detecting the end of the stream (i.e. when there isn't another message to read). I can't remember whether there's a fix for it at the moment - I have a feeling it's changed in the Java version and I may not have ported the change yet. Anyway, that's definitely the area to look at.