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How are you determining the end of the encoded protocol buffer? What language/data type are you using? It sounds to me like you are null termination (perhaps with a C char*?), which isn't going to work to well with a binary structure. Decoding with a null byte, particularly for an integer field, shouldn't ever cause a problem with protocol buffers.
Having null bytes in the encoded bytes should be expected. In C terms, assume the encoded data is an array of unsigned chars (so a null value is of no particular significance).
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